X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PZ3PDB ENTRY 1PZ3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.0M SODIUM FORMATE,0.1M SODIUM CACODYLATE PH 6.5,5% DIOXANE
Crystal Properties
Matthews coefficientSolvent content
2.957.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 173.451α = 90
b = 173.451β = 90
c = 272.203γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHTORIDAL MIRROR2005-05-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
12.963.3799.10.129.83.891349
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)
12.93.0699.60.572.33.8

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 1PZ32.9145.8686649455498.80.2040.2010.255RANDOM52.27
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]
0.930.93-1.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.538
r_dihedral_angle_3_deg17.352
r_dihedral_angle_4_deg14.972
r_dihedral_angle_1_deg6.933
r_angle_refined_deg1.335
r_scangle_it0.835
r_scbond_it0.511
r_mcangle_it0.342
r_nbtor_refined0.312
r_nbd_refined0.215
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.538
r_dihedral_angle_3_deg17.352
r_dihedral_angle_4_deg14.972
r_dihedral_angle_1_deg6.933
r_angle_refined_deg1.335
r_scangle_it0.835
r_scbond_it0.511
r_mcangle_it0.342
r_nbtor_refined0.312
r_nbd_refined0.215
r_mcbond_it0.189
r_xyhbond_nbd_refined0.166
r_symmetry_hbond_refined0.151
r_chiral_restr0.101
r_symmetry_vdw_refined0.099
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 Atoms23836
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms144

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing