X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 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
1.8834.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.35α = 90
b = 30.633β = 105.37
c = 63.729γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2008-02-20MSINGLE 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
11.215085.70.05210.13.533880-3
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)
1.211.2527.90.4451.91084

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 REPLACEMENTTHROUGHOUT1MBC1.2119.9433863168086.040.1560.1530.21RANDOM15.62
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]
0.02-0.02-0.02-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.754
r_dihedral_angle_4_deg13.62
r_dihedral_angle_3_deg13.192
r_sphericity_free11.068
r_scangle_it7.031
r_sphericity_bonded6.43
r_dihedral_angle_1_deg5.335
r_scbond_it5.228
r_mcangle_it3.684
r_rigid_bond_restr3.491
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.754
r_dihedral_angle_4_deg13.62
r_dihedral_angle_3_deg13.192
r_sphericity_free11.068
r_scangle_it7.031
r_sphericity_bonded6.43
r_dihedral_angle_1_deg5.335
r_scbond_it5.228
r_mcangle_it3.684
r_rigid_bond_restr3.491
r_mcbond_it2.617
r_angle_refined_deg2.229
r_nbtor_refined0.324
r_nbd_refined0.306
r_metal_ion_refined0.238
r_symmetry_vdw_refined0.207
r_symmetry_hbond_refined0.171
r_chiral_restr0.168
r_xyhbond_nbd_refined0.157
r_bond_refined_d0.025
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1217
Nucleic Acid Atoms
Solvent Atoms153
Heterogen Atoms55

Software

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