X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4MF7PDB ENTRY 4MF7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5Protein in 10 mM HEPES, pH 7.5, 150 mM sodium chloride, 5% glycerol, reservoir: 25% PEG4000, 0.1M TRIS-HCl pH 8.5, 0.2M calcium acetate, 5 mM GSH, cryoprotectant: 20% glycerol, vapor diffusion, sitting drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2745.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.998α = 89.98
b = 99.359β = 89.97
c = 108.734γ = 89.99
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2013-09-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

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
11.95097.20.0478.82309970-5
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)
11.91.9395.10.352.52

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 4MF71.90150303683628297.030.186580.185770.22542RANDOM31.684
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]
5.430.210.05-2.950.06-2.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.669
r_dihedral_angle_3_deg13.158
r_dihedral_angle_4_deg12.236
r_long_range_B_other10.659
r_long_range_B_refined10.639
r_scangle_other10.173
r_scbond_it9.518
r_scbond_other9.512
r_mcangle_other5.65
r_mcangle_it5.649
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.669
r_dihedral_angle_3_deg13.158
r_dihedral_angle_4_deg12.236
r_long_range_B_other10.659
r_long_range_B_refined10.639
r_scangle_other10.173
r_scbond_it9.518
r_scbond_other9.512
r_mcangle_other5.65
r_mcangle_it5.649
r_dihedral_angle_1_deg5.502
r_mcbond_it5.16
r_mcbond_other5.157
r_angle_refined_deg1.381
r_angle_other_deg0.811
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms29909
Nucleic Acid Atoms
Solvent Atoms2214
Heterogen Atoms314

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling