X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 298.0
Details PEG 3350, sodium acetate, Tris hydrochloride, pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.17 α = 90
b = 63.17 β = 90
c = 100.38 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
IMAGE PLATE MARRESEARCH Flat mirror(vertical) single crystal (Si311) bent monochromator (horizontal) 2000-05-26
Diffraction Radiation
Monochromator Protocol
bent crystal Si(311) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 1.5498, 1.7377, 1.7401, 1.9075 SSRL BL9-1

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
1.5 44.67 0.946 0.047 -- -- 5.1 31486 31486 0.0 0.0 23.743
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)
1.5 1.53 92.1 0.532 -- 2.1 2.5 1381

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
MAD 1.5 53.45 0.0 0.0 29881 29881 1605 94.61 0.2289 0.2289 0.227 0.26 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 1.5 1.539 2212 107 -- 0.238 0.281 0.0 93.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 22.9
Anisotropic B[1][1] 0.17
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.33
RMS Deviations
Key Refinement Restraint Deviation
p_torsion1_d 3.4
p_angle_d 1.543
p_bond_d 0.017
p_torsion3_d 15.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.134
Luzzati Sigma A (Observed) 0.097
Luzzati ESD (R-Free Set) 0.102
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1576
Nucleic Acid Atoms 0
Heterogen Atoms 43
Solvent Atoms 244

Software

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