X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 294.0
Details PEG 400, ammonium sulfate, Tris-base, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.12 α = 90
b = 97.12 β = 90
c = 61.41 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD PHILLIPS -- 2002-03-07
Diffraction Radiation
Monochromator Protocol
Si III Channel SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12C 0.9202 NSLS X12C

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
1.7 30 99.96 0.045 -- -- 14.1 32880 32880 0.0 0.0 15.319
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)
1.7 1.76 100.0 0.187 -- 16.7 -- 3249

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
SAD 1.7 30.02 -- 0.0 32880 30783 1650 98.8 0.18358 0.18358 0.18218 0.21016 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 1.7 1.745 -- 114 2183 0.16 0.197 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.666
Anisotropic B[1][1] -0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.03
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.839
r_scbond_it 2.292
r_mcangle_it 1.603
r_mcbond_it 0.898
r_symmetry_hbond_refined 0.144
r_symmetry_vdw_other 0.291
r_symmetry_vdw_refined 0.31
r_bond_refined_d 0.01
r_bond_other_d 0.001
r_angle_refined_deg 1.466
r_angle_other_deg 0.921
r_dihedral_angle_1_deg 4.899
r_dihedral_angle_2_deg 16.844
r_chiral_restr 0.231
r_gen_planes_refined 0.006
r_gen_planes_other 0.003
r_nbd_refined 0.271
r_nbd_other 0.212
r_xyhbond_nbd_refined 0.131
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1788
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 136

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
SOLVE model building
SCALEPACK data reduction
DENZO data collection