X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 277.0
Details 0.1M Tris pH8.5, 2.5M Ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 106.04 α = 90
b = 106.04 β = 90
c = 182.97 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC-3 mirror 2009-04-18
Diffraction Radiation
Monochromator Protocol
Si 111 crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.97954, 0.97986 APS 19-BM

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
2.43 50 99.8 0.146 -- -- 9.7 40035 40035 -- -- --
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)
2.43 2.47 96.1 0.767 -- 4.41 7.7 1896

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 2.43 50.0 -- -- -- 37255 1965 97.95 -- 0.18171 0.17915 0.23079 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 2.431 2.494 -- 126 2566 0.262 0.348 -- 92.67
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.654
Anisotropic B[1][1] -1.16
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.32
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.005
r_mcangle_it 1.177
r_dihedral_angle_1_deg 5.913
r_chiral_restr 0.091
r_dihedral_angle_2_deg 39.667
r_angle_refined_deg 1.297
r_mcbond_it 0.602
r_scangle_it 3.176
r_bond_refined_d 0.011
r_dihedral_angle_3_deg 14.683
r_scbond_it 1.875
r_dihedral_angle_4_deg 20.381
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5121
Nucleic Acid Atoms 0
Heterogen Atoms 114
Solvent Atoms 492

Software

Software
Software Name Purpose
SBC-Collect data collection version: collect
SHELXD phasing
MLPHARE phasing
ARP model building
WARP model building
HKL-3000 phasing
REFMAC refinement version: 5.5.0102
HKL-3000 data reduction
HKL-3000 data scaling