X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 297.0
Details 24% PEG 1500, 20% Glycerol, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 105.84 α = 90
b = 88.51 β = 109.97
c = 123 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-02-06
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97931, 0.97948 APS 19-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 50 99.9 0.102 -- -- 7.5 143525 143525 -- -3.0 28.1
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)
2.0 2.03 100.0 0.642 -- -- 7.5 7138

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
MAD 2.0 41.33 -- 0.0 143358 143358 7172 99.47 0.1579 0.1579 0.1559 0.1957 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 2.0 2.052 -- 511 9681 0.207 0.26 -- 96.41
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.2349
Anisotropic B[1][1] 1.58
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.28
Anisotropic B[2][2] 1.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.46
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.008
r_chiral_restr 0.098
r_dihedral_angle_4_deg 20.974
r_dihedral_angle_3_deg 13.88
r_dihedral_angle_2_deg 34.775
r_dihedral_angle_1_deg 6.141
r_angle_other_deg 0.831
r_angle_refined_deg 1.659
r_bond_other_d 0.001
r_bond_refined_d 0.015
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14395
Nucleic Acid Atoms 0
Heterogen Atoms 90
Solvent Atoms 1201

Software

Computing
Computing Package Purpose
SBC-Collect Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
HKL-3000, SHELXD, SHELXE, MLPHARE, DM, SOLVE/RESOLVE, ARP/WARP, CCP4, O, COOT Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
HKL data reduction