X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Details PROTEIN WAS CRYSTALLIZED FROM 17% PEG-MME 5000, 400 MM AMMONIUM ACETATE, 5% GLYCEROL, 10 MM SODIUM AZIDE, PH 6.5.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.15 α = 90
b = 83.05 β = 90
c = 111.11 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS II COLLIMATOR 1995-06
Diffraction Radiation
Monochromator Protocol
GRAPHITE(002) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R -- -- --

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
2.4 40 96.9 0.051 -- -- 5.1 -- 20693 -- -- 25.8
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)
2.4 2.46 90.0 0.154 -- 6.0 4.2 --

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
MIR, MOLECULAR REPLACEMENT 2.4 40.0 -- 0.0 -- 20663 2018 97.0 -- 0.195 0.195 0.25 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 2.4 2.44 -- 101 787 0.254 0.338 0.034 86.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 21.5
Anisotropic B[1][1] -22.92
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.74
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.51
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 2.84
x_scbond_it 2.37
x_mcangle_it 1.76
x_mcbond_it 1.33
x_improper_angle_d 1.06
x_bond_d 0.006
x_angle_deg 1.245
x_dihedral_angle_d 24.9
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Luzzati Sigma A (Observed) 0.24
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.34
Luzzati Sigma A (R-Free Set) 0.27
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3757
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 258

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR 3.8 Structure Solution
X-PLOR 3.8 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.8 refinement
X-PLOR version: 3.8 model building
SCALEPACK data reduction
DENZO data collection