X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 295.0
Details 15% PEG 6000, 0.1M Bicine pH 8.5, vapor diffusion, sitting drop, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.78 α = 90
b = 99.2 β = 90
c = 118.07 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2009-04-07
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID

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
2.05 50 93.5 0.068 -- -- 5.7 -- 52419 -- -- --
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)
2.05 2.12 66.7 0.419 -- -- 3.8 3690

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 2.05 50.0 -- 0.0 -- 52318 2683 93.45 -- 0.2 0.198 0.238 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 2.048 2.101 -- 153 2500 0.277 0.309 -- 65.04
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.009
Anisotropic B[1][1] -1.82
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.43
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.25
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.414
r_gen_planes_refined 0.004
r_dihedral_angle_2_deg 36.665
r_mcbond_it 0.694
r_scbond_it 2.078
r_xyhbond_nbd_refined 0.152
r_mcangle_it 1.128
r_nbtor_refined 0.3
r_dihedral_angle_4_deg 17.133
r_symmetry_hbond_refined 0.139
r_symmetry_vdw_refined 0.148
r_dihedral_angle_3_deg 17.29
r_scangle_it 3.573
r_dihedral_angle_1_deg 5.894
r_nbd_refined 0.195
r_chiral_restr 0.097
r_bond_refined_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6143
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 310

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.005
HKL-2000 data reduction
HKL-2000 data scaling
MOLREP phasing