X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 293.0
Details 50mg/ml HEWL, 20%(w/v) PEG4000, 100mM sodium citrate (pH 5.5), 100mM sodium iodide, and 20%(v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.35 α = 90
b = 78.35 β = 90
c = 37.54 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
CCD MARRESEARCH -- 2001-04-26
Diffraction Radiation
Monochromator Protocol
Si (111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.5400, 0.3746, 0.3734 SPRING-8 BL41XU

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
1.6 25 99.5 -- 0.061 -- 12.1 15776 15776 0.0 0.0 16.4
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)
1.6 1.66 99.9 -- 0.212 5.5 -- 1539

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 1.6 25.0 -- 0.0 15774 15774 775 99.6 -- -- 0.205 0.232 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 1.6 1.7 2320 123 -- 0.221 0.284 0.019 93.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 16.3
Anisotropic B[1][1] -0.14
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.28
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.004
c_angle_deg 1.3
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.18
Luzzati Sigma A (Observed) 0.08
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.21
Luzzati Sigma A (R-Free Set) 0.16
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 995
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 94

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHARP Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
CNS refinement
SHARP model building
SCALEPACK data reduction
HKL-2000 data collection