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
1.8734.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.343α = 90
b = 30.613β = 105.86
c = 63.785γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray140CCDMAR 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
11.215089.40.0528.63.435428-3
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)
1.211.2535.80.4771.61402

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 REPLACEMENTTHROUGHOUT1MBC1.2117.0135405176390.540.1580.1560.209RANDOM15.802
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]
-0.010.02-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.848
r_dihedral_angle_4_deg22.246
r_dihedral_angle_3_deg14.052
r_sphericity_free11.792
r_scangle_it6.875
r_sphericity_bonded6.64
r_dihedral_angle_1_deg5.433
r_scbond_it5.256
r_mcangle_it3.688
r_rigid_bond_restr3.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.848
r_dihedral_angle_4_deg22.246
r_dihedral_angle_3_deg14.052
r_sphericity_free11.792
r_scangle_it6.875
r_sphericity_bonded6.64
r_dihedral_angle_1_deg5.433
r_scbond_it5.256
r_mcangle_it3.688
r_rigid_bond_restr3.31
r_mcbond_it2.773
r_angle_refined_deg2.394
r_metal_ion_refined0.611
r_nbtor_refined0.328
r_nbd_refined0.307
r_symmetry_hbond_refined0.247
r_symmetry_vdw_refined0.207
r_chiral_restr0.183
r_xyhbond_nbd_refined0.128
r_bond_refined_d0.029
r_gen_planes_refined0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1217
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms55

Software

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