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 GROWN BY REPEATED MACROSEEDING, TRANSFORMED TO LOW HUMIDITY FORM AND FLASH COOLED, 1-2% V/V OF GLYCEROL WAS ADDED TO SODIUM CITRATE TO PREVENT THE CRYSTAL CRACKING DURING THE FLASH COOLING

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.72 α = 90
b = 28.25 β = 90.87
c = 44.13 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 1998-05-29
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
1.68 50 99.1 0.1 -- -- 4.244 -- 11033 -- 0.0 13.4
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)
1.68 1.74 97.9 0.446 -- 1.904 3.53 --

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 1.68 44.12 -- 0.0 -- 11022 570 98.8 -- 0.193 0.193 0.21 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 1.68 1.79 -- 77 1702 0.31 0.264 0.03 96.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 18.3
Anisotropic B[1][1] 1.6
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.64
Anisotropic B[2][2] 0.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.77
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 4.92
c_scbond_it 3.21
c_mcangle_it 2.5
c_mcbond_it 1.74
c_improper_angle_d 0.8
c_bond_d 0.005
c_angle_deg 1.3
c_dihedral_angle_d 19.5
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Sigma A (Observed) 0.25
Luzzati Resolution Cutoff (Low) 50.0
Luzzati ESD (R-Free Set) 0.21
Luzzati Sigma A (R-Free Set) 0.21
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 867
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 60

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