X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.7
Temperature 293.0
Details PEG 8000, sodium acetate, DTT, sucrose monolaurate, MES, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 99.3 α = 90
b = 66.7 β = 105.7
c = 92.56 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirrors 2001-04-17
Diffraction Radiation
Monochromator Protocol
Double-crystal, fixed-exit Si-III SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12B 0.9796 NSLS X12B

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
1.85 25 97.6 0.051 -- -- 3.0 -- 46338 -- -3.0 16.5
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)
1.85 1.92 96.4 0.217 -- 3.0 3.0 4557

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 1.88 24.56 -- 0.0 -- 45225 1808 94.4 -- 0.185 0.185 0.217 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 1.88 1.99 -- 273 6651 0.22 0.234 0.014 87.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 18.0
Anisotropic B[1][1] -0.38
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.16
Anisotropic B[2][2] -3.52
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.9
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 1.85
c_scangle_it 2.63
c_dihedral_angle_d 24.9
c_mcangle_it 1.86
c_angle_deg 1.4
c_improper_angle_d 0.81
c_mcbond_it 1.25
c_bond_d 0.006
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Sigma A (Observed) 0.13
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.23
Luzzati Sigma A (R-Free Set) 0.13
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3804
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 481

Software

Software
Software Name Purpose
AMoRE phasing
CNS refinement version: 1.0
DENZO data reduction
SCALEPACK data scaling