X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DV2PDB ENTRY 1DV2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1WELL: 0.1 M POTASSIUM CHLORIDE, 4% (W/V) PEG 8000 PROTEIN: 12 MG/ML, 250 MM POTASSIUM CHLORIDE, 10 MM HEPES, PH 7.2
Crystal Properties
Matthews coefficientSolvent content
2.7554.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.19α = 90
b = 106.203β = 90
c = 123.055γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-BMAPS17-BM

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
12.45093.20.111.284.0640822
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)
12.42.4971.30.233.383.2

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 1DV22.480.3238720205593.20.210.2080.248RANDOM34.2
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]
-0.16-0.070.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.452
r_dihedral_angle_4_deg17.329
r_dihedral_angle_3_deg15.229
r_dihedral_angle_1_deg5.089
r_scangle_it1.522
r_angle_refined_deg1.023
r_scbond_it0.895
r_mcangle_it0.606
r_mcbond_it0.358
r_nbtor_refined0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.452
r_dihedral_angle_4_deg17.329
r_dihedral_angle_3_deg15.229
r_dihedral_angle_1_deg5.089
r_scangle_it1.522
r_angle_refined_deg1.023
r_scbond_it0.895
r_mcangle_it0.606
r_mcbond_it0.358
r_nbtor_refined0.294
r_nbd_refined0.173
r_symmetry_vdw_refined0.161
r_xyhbond_nbd_refined0.128
r_symmetry_hbond_refined0.122
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms6850
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing