X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DZRPDB ENTRY 1DZR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.50.5 + 0.5 UL SITTING DROPS IN INTELLIPLATES, 0.1 M NA-CITRATE BUFFER, PH 5.5, 46% PEG-MME 2K AND 3 % LDAO B-MERCAPTO-ETHANOL IN PROTEIN STOCK
Crystal Properties
Matthews coefficientSolvent content
2.1442.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.905α = 90
b = 64.905β = 90
c = 87.203γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC CCDMIRRORS2001-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.3ALS5.0.3

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
11.755.999.20.05246.822.3823837
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)
11.71.7693.80.412.491.7

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 1DZR1.72522589113899.30.2030.2010.249RANDOM25.55
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]
-0.52-0.26-0.520.79
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it6.599
r_dihedral_angle_1_deg6.411
r_scbond_it4.97
r_mcangle_it3.587
r_mcbond_it2.607
r_angle_refined_deg1.757
r_angle_other_deg0.927
r_symmetry_vdw_other0.314
r_nbd_other0.259
r_nbd_refined0.205
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it6.599
r_dihedral_angle_1_deg6.411
r_scbond_it4.97
r_mcangle_it3.587
r_mcbond_it2.607
r_angle_refined_deg1.757
r_angle_other_deg0.927
r_symmetry_vdw_other0.314
r_nbd_other0.259
r_nbd_refined0.205
r_symmetry_vdw_refined0.179
r_xyhbond_nbd_refined0.173
r_symmetry_hbond_refined0.155
r_chiral_restr0.11
r_nbtor_other0.094
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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 Atoms1564
Nucleic Acid Atoms
Solvent Atoms274
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
EPMRphasing