X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Details PROTEIN WAS CRYSTALLIZED FROM 18% PEG 8,000, 100MM SODIUM CACODYLATE PH 6.5, 200MM CALCIUM ACETATE, 1MM EDTA, 4MM DTT, 40MM D-INOSITOL-1-PHOSPHATE, 0.1M SODIUM CACODYLATE PH 6.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.37 α = 90
b = 86.37 β = 90
c = 153.79 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 273
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR SIEMENS COLLIMATOR 1993-09
Diffraction Radiation
Monochromator Protocol
GRAPHITE(002) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE MACSCIENCE M18XH -- -- --

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
2.5 10 87.0 0.073 -- -- 3.3 -- 20214 -- 0.0 22.5
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)
2.5 2.6 79.6 0.243 -- -- 2.9 --

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 2.5 10.0 -- 2.0 -- 18342 1814 79.0 -- 0.153 0.153 0.189 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 2.5 2.65 -- 240 2152 0.197 0.219 0.014 62.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 18.9
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 7.66
x_scbond_it 5.05
x_mcangle_it 3.89
x_mcbond_it 2.6
x_improper_angle_d 1.16
x_bond_d 0.006
x_angle_deg 1.4
x_dihedral_angle_d 23.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.21
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.24
Luzzati Sigma A (R-Free Set) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4144
Nucleic Acid Atoms 0
Heterogen Atoms 40
Solvent Atoms 320

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
X-PLOR 3.1 Structure Solution
X-PLOR 3.1 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.1 refinement
X-PLOR version: 3.1 model building
XSCALE data reduction
XDS data collection