X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 295.0
Details PEG, Tris, DTT, isopropanol at pH 8.0, VAPOR DIFFUSION, HANGING DROP at 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.88 α = 109.53
b = 141.05 β = 105.83
c = 158.11 γ = 101.33
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD CUSTOM-MADE -- 2001-03-12
CCD ADSC QUANTUM 4 -- 2001-02-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.100 NSLS X25
SYNCHROTRON NSLS BEAMLINE X26C 1.100 NSLS X26C

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
2.7 50 99.2 -- 0.17 -- 3.8 187987 187987 -- -1000.0 --
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)
2.7 2.8 -- -- 0.73 2.7 -- --

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 2.7 50.0 -- 0.0 178563 178563 9424 99.18 0.215 0.21505 0.21311 0.25154 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 2.7 2.77 -- 688 13129 0.286 0.377 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.67
Anisotropic B[1][1] 1.31
Anisotropic B[1][2] 0.3
Anisotropic B[1][3] 0.37
Anisotropic B[2][2] -1.57
Anisotropic B[2][3] -0.91
Anisotropic B[3][3] -0.03
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.576
r_scbond_it 3.409
r_mcangle_it 2.03
r_mcbond_it 1.068
r_symmetry_hbond_refined 0.291
r_xyhbond_nbd_refined 0.177
r_nbd_refined 0.177
r_gen_planes_refined 0.009
r_chiral_restr 0.142
r_angle_refined_deg 2.346
r_bond_refined_d 0.025
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 36348
Nucleic Acid Atoms 0
Heterogen Atoms 360
Solvent Atoms 123

Software

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