X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.5
Details PROTEIN WAS CRYSTALLIZED FROM 12% PEG3000, 0.25M SODIUM GLUTAMATE, 100MM CACODYLIC ACID, PH 5.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 255.26 α = 90
b = 265.25 β = 90
c = 184.4 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MIRRORS 1996-09
Diffraction Radiation
Monochromator Protocol
TWO CRYSTAL NON-DISPERSIVE --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 -- NSLS X25

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
3 99 96.7 -- 0.121 -- 3.3 -- 242684 -- -- --
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)
3.0 3.14 91.2 -- 0.53 1.8 2.4 --

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 3.0 40.0 -- 2.0 -- 198459 9846 79.7 -- 0.248 0.248 0.291 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 3.0 3.14 -- 827 16487 0.356 0.389 -- 56.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 61.5
Anisotropic B[1][1] 14.83
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 12.27
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -27.1
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 6.0
x_scbond_it 4.04
x_mcangle_it 4.32
x_mcbond_it 2.71
x_improper_angle_d 0.71
x_bond_d 0.01
x_angle_deg 1.472
x_dihedral_angle_d 19.6
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.45
Luzzati Sigma A (Observed) 0.58
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.51
Luzzati Sigma A (R-Free Set) 0.65
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 58674
Nucleic Acid Atoms 0
Heterogen Atoms 196
Solvent Atoms 0

Software

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