X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 295.5
Details 1.9 M sodium formate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.5K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 87.9 α = 90
b = 92.9 β = 90
c = 118 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 200
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 KOHZU: Double Crystal Si(111) 2005-11-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 ALS 8.2.1

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
2.5 50 99.2 -- 0.076 -- 4.6 34006 33730 2.0 -- 31.3
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)
2.5 2.59 95.5 -- 0.454 1.9 3.2 3232

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 2.5 50.0 -- 2.0 34006 26790 1309 78.4 -- -- 0.212 0.251 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 2.5 2.59 1260 54 -- 0.263 0.256 0.035 95.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 49.5
Anisotropic B[1][1] -3.82
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.65
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.17
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 23.2
c_bond_d 0.008
c_angle_d 1.6
c_improper_angle_d 0.96
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.31
Luzzati Sigma A (Observed) 0.29
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.38
Luzzati Sigma A (R-Free Set) 0.28
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4878
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 181

Software

Software
Software Name Purpose
ADSC data collection version: Quantum
AMoRE phasing
CNS refinement version: 1.0
HKL-2000 data reduction
HKL-2000 data scaling