X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.9
Temperature 293.0
Details 100 mM HEPES, 12% (w:v) PEG2000, 5% (w:v) MPD, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 117.2 α = 90
b = 85.3 β = 90
c = 42.6 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Yale Mirrors 2004-05-30
Diffraction Radiation
Monochromator Protocol
Yale Mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 1.5418 -- --

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
2.6 20 89.1 0.129 0.129 -- 5.9 13969 12405 0.0 0.0 39.0
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)
2.6 2.72 92.9 0.615 0.615 2.66 -- --

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 2.6 20.0 -- 0.0 11808 11652 592 85.1 0.252 0.252 0.218 0.269 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 2.6 2.68 986 40 946 0.353 0.345 -- --
X Ray Diffraction 2.68 2.78 995 58 937 0.332 0.373 -- --
X Ray Diffraction 2.78 2.89 1026 66 960 0.312 0.313 -- --
X Ray Diffraction 2.89 3.02 1048 51 997 0.286 0.359 -- --
X Ray Diffraction 3.02 3.18 1043 39 1004 0.269 0.345 -- --
X Ray Diffraction 3.18 3.38 1044 40 1004 0.237 0.277 -- --
X Ray Diffraction 3.38 3.64 1019 58 961 0.232 0.301 -- --
X Ray Diffraction 3.64 4.0 1017 56 961 0.171 0.221 -- --
X Ray Diffraction 4.0 4.57 1022 48 974 0.171 0.246 -- --
X Ray Diffraction 4.57 5.74 1127 55 1072 0.193 0.242 -- --
X Ray Diffraction 5.74 20.0 1325 81 1244 0.194 0.244 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Anisotropic, restrained
Mean Isotropic B 52.628
Anisotropic B[1][1] -23.064
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 17.182
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.882
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.4
c_dihedral_angle_d 25.0
c_bond_d 0.008
c_improper_angle_d 0.92
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.35
Luzzati Sigma A (Observed) 0.5
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.43
Luzzati Sigma A (R-Free Set) 0.51
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3170
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 114

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
CNS refinement
PDB_EXTRACT data extraction version: 1.701