X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8.4
Details PROTEIN WAS CRYSTALLIZED FROM @M NA/K2 PHOSPHATE, 50MM TRIS-HCL, PH 8.4

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 163.07 α = 90
b = 90.07 β = 90
c = 111.89 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
X RAY IMAGE INTENSIFIER (THOMPSON) +PRINCETON CCD DETECTOR THOMPSON FOCUSED BEAM TOROIDAL MIRROR 1997-01
Diffraction Radiation
Monochromator Protocol
LAUE BRAGG --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID09 -- ESRF ID09

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
2.15 30 99.3 0.063 0.063 -- 3.8 -- 91663 -- 2.0 36.18
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)
2.15 2.27 96.9 0.214 0.214 3.4 3.3 --

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 2.15 30.0 -- 2.5 -- 82362 2937 89.0 -- 0.209 0.209 0.242 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 2.15 2.25 -- 341 8554 0.2517 0.3235 0.017 78.02
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 39.1
Anisotropic B[1][1] 3.2
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.416
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.18
RMS Deviations
Key Refinement Restraint Deviation
x_bond_d 0.014
x_angle_deg 1.857
x_mcbond_it 2.0
x_scbond_it 3.2
x_improper_angle_d 1.342
x_dihedral_angle_d 26.59
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.32
Luzzati Resolution Cutoff (Low) 30.0
Luzzati ESD (R-Free Set) 0.34
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8415
Nucleic Acid Atoms 0
Heterogen Atoms 198
Solvent Atoms 870

Software

Software
Software Name Purpose
AMoRE phasing
X-PLOR refinement version: 3.8
DENZO data reduction
PROW data reduction
CCP4 data scaling