X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.3
Temperature 296.0
Details PEG 8000, citrate-phosphate buffer, sodium azide, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 296K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 112.73 α = 90
b = 137.27 β = 95.53
c = 61.88 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 296
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Focusing mirrors 1997-09-12
Diffraction Radiation
Monochromator Protocol
Focusing mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200H 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
2.1 40 93.8 0.078 -- -- 2.0 50811 43096 2.0 1.0 --
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)
2.1 2.18 94.1 0.355 -- 2.1 2.0 5095

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 2.1 8.0 -- 2.0 50811 43096 4338 80.5 0.256 0.232 0.199 0.295 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 2.1 2.23 4769 538 -- 0.1989 0.2953 -- --
X Ray Diffraction 2.23 2.4 5856 642 -- 0.1935 0.2933 -- --
X Ray Diffraction 2.4 2.63 6521 691 -- 0.1857 0.2908 -- --
X Ray Diffraction 2.63 2.99 6849 796 -- 0.1753 0.285 -- --
X Ray Diffraction 2.99 3.71 7284 838 -- 0.1619 0.2761 -- --
X Ray Diffraction 3.71 8.0 7479 833 2671 0.1498 0.2611 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 31.9
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 1.39
x_dihedral_angle_d 24.8
x_angle_deg 1.63
x_bond_d 0.008
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.26
Luzzati Resolution Cutoff (Low) 8.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6778
Nucleic Acid Atoms 0
Heterogen Atoms 23
Solvent Atoms 512

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
X-PLOR model building
SCALEPACK data reduction
DENZO data collection