X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MBCPDB ENTRY 1MBC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1batch62932.4M Ammonium sulfate, 10mM TrisHCl, 100mM Sodium phosphate, pH 6.0, batch, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.8934.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.462α = 90
b = 30.714β = 105.62
c = 63.932γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDMAR CCD 165 mm2007-05-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW14A0.827Photon FactoryAR-NW14A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.215095.90.05510.73.538082-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.211.2564.60.4112.22544

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1MBC1.2120.0238066191396.660.1470.1450.188RANDOM15.135
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.020.01-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.81
r_dihedral_angle_4_deg19.367
r_dihedral_angle_3_deg14.177
r_sphericity_free10.385
r_scangle_it6.441
r_sphericity_bonded5.924
r_scbond_it4.941
r_dihedral_angle_1_deg4.844
r_rigid_bond_restr3.769
r_mcangle_it3.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.81
r_dihedral_angle_4_deg19.367
r_dihedral_angle_3_deg14.177
r_sphericity_free10.385
r_scangle_it6.441
r_sphericity_bonded5.924
r_scbond_it4.941
r_dihedral_angle_1_deg4.844
r_rigid_bond_restr3.769
r_mcangle_it3.298
r_mcbond_it2.308
r_angle_refined_deg1.98
r_metal_ion_refined0.535
r_nbtor_refined0.319
r_nbd_refined0.306
r_symmetry_vdw_refined0.167
r_chiral_restr0.138
r_symmetry_hbond_refined0.131
r_xyhbond_nbd_refined0.127
r_bond_refined_d0.022
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1217
Nucleic Acid Atoms
Solvent Atoms160
Heterogen Atoms55

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling