X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 291.0
Details 0.1 M Tris, 2.0 M NH4H2PO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.97 α = 90
b = 82.97 β = 90
c = 101.89 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2008-12-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 1.0 SSRL BL7-1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.1 41.48 92.7 0.052 0.052 -- 11.6 -- 77795 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.1 1.16 65.1 0.407 0.407 1.9 4.3 7781

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.1 41.48 -- 0.0 -- 77748 3940 92.52 -- 0.12 0.119 0.142 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.1 1.129 -- 185 3476 0.258 0.309 -- 60.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 10.649
Anisotropic B[1][1] -0.32
Anisotropic B[1][2] -0.16
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.32
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.48
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 16.418
r_dihedral_angle_1_deg 12.638
r_mcbond_other 0.871
r_symmetry_vdw_other 0.274
r_gen_planes_other 0.01
r_symmetry_hbond_refined 0.251
r_chiral_restr 0.117
r_angle_other_deg 1.546
r_sphericity_free 12.4
r_angle_refined_deg 2.016
r_xyhbond_nbd_refined 0.383
r_symmetry_vdw_refined 0.246
r_nbd_refined 0.306
r_sphericity_bonded 4.843
r_rigid_bond_restr 1.804
r_nbd_other 0.204
r_nbtor_other 0.094
r_mcangle_it 2.61
r_mcbond_it 2.118
r_bond_refined_d 0.021
r_dihedral_angle_2_deg 39.311
r_gen_planes_refined 0.011
r_bond_other_d 0.005
r_dihedral_angle_3_deg 10.632
r_scangle_it 4.303
r_nbtor_refined 0.184
r_scbond_it 3.655
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1696
Nucleic Acid Atoms 0
Heterogen Atoms 23
Solvent Atoms 338

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling version: 3.2.25
PHASER phasing version: 1.3.3
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005