X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J4DPDB ENTRY 2J4D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.610 MG/ML PROTEIN, 85 MM NA-CITRATE PH 4.6, 170 MM NH4-ACETATE, 21.5% (W/V) PEG 4000 AND 15% (V/V) GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
2.3647.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.734α = 90
b = 136.082β = 90
c = 211.484γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2007-01-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7AEMBL/DESY, HAMBURGBW7A

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
1215.199.20.114.96.02229217-3
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)
122.0589.60.412.8

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 2J4D2.0115.03227588151899.20.1850.1840.222RANDOM35.98
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]
-0.08-0.020.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.206
r_dihedral_angle_4_deg18.282
r_dihedral_angle_3_deg12.852
r_dihedral_angle_1_deg5.451
r_scangle_it1.622
r_angle_refined_deg1.151
r_scbond_it1.014
r_angle_other_deg0.867
r_mcangle_it0.8
r_mcbond_it0.471
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.206
r_dihedral_angle_4_deg18.282
r_dihedral_angle_3_deg12.852
r_dihedral_angle_1_deg5.451
r_scangle_it1.622
r_angle_refined_deg1.151
r_scbond_it1.014
r_angle_other_deg0.867
r_mcangle_it0.8
r_mcbond_it0.471
r_symmetry_vdw_refined0.246
r_symmetry_vdw_other0.217
r_nbd_refined0.197
r_nbd_other0.183
r_nbtor_refined0.18
r_symmetry_hbond_refined0.171
r_xyhbond_nbd_refined0.131
r_nbtor_other0.079
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms23956
Nucleic Acid Atoms520
Solvent Atoms1305
Heterogen Atoms528

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing