X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4J8FPDB entry 4J8F

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72912.15 Na-malonate, pH 7.0, vapor diffusion, hanging drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.5852.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.29α = 90
b = 126.998β = 105.93
c = 57.312γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-08-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9189ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.863.49998.70.118.33.11924719247-1-1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.95960.4270.4271.83.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 4J8F2.820185331823593398.40.2490.2460.299RANDOM36.26
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]
-34.18-5.7565.9-31.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.373
r_dihedral_angle_3_deg20.199
r_dihedral_angle_4_deg17.541
r_dihedral_angle_1_deg4.863
r_scangle_it1.237
r_angle_refined_deg1.039
r_scbond_it0.688
r_mcangle_it0.528
r_mcbond_it0.278
r_chiral_restr0.068
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.373
r_dihedral_angle_3_deg20.199
r_dihedral_angle_4_deg17.541
r_dihedral_angle_1_deg4.863
r_scangle_it1.237
r_angle_refined_deg1.039
r_scbond_it0.688
r_mcangle_it0.528
r_mcbond_it0.278
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4884
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XSCALEdata scaling