X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Details PROTEIN WAS CRYSTALLIZED FROM 2% PEG 4000, 50 MM PIPES PH 6.5, 350 MM LI2SO4, THEN STABILIZED IN THE SAME BUFFER WITH 21% ETHYLENE GLYCOL

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.12 α = 90
b = 64.44 β = 95.74
c = 69.95 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH SILICON CRYSTAL 1997-09-12
Diffraction Radiation
Monochromator Protocol
SI(111) --
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
1.8 40 93.2 0.055 0.076 -- 3.2 -- 42976 -- 2.0 27.0
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)
1.8 1.86 95.9 0.055 0.319 3.4 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
MAD, MIR 1.8 40.0 -- 2.0 -- 40453 4081 84.6 -- 0.1905 0.1905 0.227 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 1.8 1.86 -- 335 2998 0.208 0.252 -- 70.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 32.8
Anisotropic B[1][1] -5.368
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -3.239
Anisotropic B[2][2] -0.11
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.478
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 6.208
c_scbond_it 4.912
c_mcangle_it 3.286
c_mcbond_it 2.902
c_improper_angle_d 0.904
c_bond_d 0.008
c_angle_deg 1.392
c_dihedral_angle_d 17.18
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.11
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.25
Luzzati Sigma A (R-Free Set) 0.13
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4036
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 180

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
DPHASE Structure Solution
CNS 0.1 Structure Refinement
Software
Software Name Purpose
CNS version: 0.1 refinement
DPHASE model building