X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.8
Details 1.6-1.7 M SODIUM CITRATE PH 6.8, PROTEIN CONCENTRATION 15 MG/ML, CRYSTAL WAS TRANSFORMED TO LOW HUMIDITY FORM AND FLASH COOLED, 1-2% V/V OF GLYCEROL WAS ADDED TO PREVENT THE CRYSTAL CRACKING DURING THE FLASH COOLING

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 26.27 α = 90
b = 35.3 β = 93.37
c = 24.04 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 1999-04-27
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44B2 -- SPRING-8 BL44B2

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 20 93.9 0.077 -- -- 2.959 -- 5574 -- 0.0 18.9
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 72.5 0.204 -- 2.279 2.43 --

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 1.6 19.85 -- 0.0 -- 5531 306 94.0 -- 0.192 0.192 0.223 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 -- 35 724 0.272 0.28 0.047 78.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 22.9
Anisotropic B[1][1] 6.44
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -3.84
Anisotropic B[2][2] -4.79
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.65
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 4.98
c_scbond_it 3.23
c_mcangle_it 2.86
c_mcbond_it 1.84
c_improper_angle_d 0.62
c_bond_d 0.004
c_angle_deg 0.9
c_dihedral_angle_d 18.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.18
Luzzati Sigma A (Observed) 0.19
Luzzati Resolution Cutoff (Low) 20.0
Luzzati ESD (R-Free Set) 0.2
Luzzati Sigma A (R-Free Set) 0.16
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 433
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 42

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
X-PLOR model building