X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WDNPDB ENTRY 1WDN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5291PEG3350, NaCl, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.346.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.863α = 90
b = 88.787β = 107.81
c = 72.11γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Sagitally focusing Ge(220) and a multilayer2004-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.93400ESRFID14-1

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
122078.80.0714.723008430084
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)
122.0360.90.5291.91.91158

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1WDN219.92284442844415181000.180110.180110.177380.2297RANDOM32.135
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]
0.85-2.61-1.35-1.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.935
r_dihedral_angle_3_deg14.512
r_dihedral_angle_4_deg11.504
r_dihedral_angle_1_deg6.374
r_scangle_it1.958
r_angle_refined_deg1.318
r_scbond_it1.304
r_angle_other_deg0.786
r_mcangle_it0.696
r_mcbond_it0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.935
r_dihedral_angle_3_deg14.512
r_dihedral_angle_4_deg11.504
r_dihedral_angle_1_deg6.374
r_scangle_it1.958
r_angle_refined_deg1.318
r_scbond_it1.304
r_angle_other_deg0.786
r_mcangle_it0.696
r_mcbond_it0.55
r_symmetry_vdw_other0.225
r_symmetry_vdw_refined0.2
r_nbd_refined0.198
r_symmetry_hbond_refined0.196
r_nbtor_refined0.175
r_nbd_other0.173
r_xyhbond_nbd_refined0.171
r_mcbond_other0.119
r_nbtor_other0.085
r_chiral_restr0.078
r_bond_refined_d0.011
r_gen_planes_refined0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3944
Nucleic Acid Atoms
Solvent Atoms324
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing