X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.8
Temperature 277.0
Details Lyophilized protein was dissolved in 100 mM sodium acetate buffer pH 4.8 containing 20 mM CaCl2. Droplets were equilibrated against 1 ml of reservoir with analogous buffer/CaCl2 solution. After 2 and 4 days, the reservoir solution was supplemented with 100 microliters of MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 140.53 α = 90
b = 140.53 β = 90
c = 140.53 γ = 90
Symmetry
Space Group I 4 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 2000-09-30
Diffraction Radiation
Monochromator Protocol
monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8423 EMBL/DESY, HAMBURG BW7B

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 40 99.2 0.07 -- -- 19.9 8429 8429 0.0 0.0 40.6
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 2.59 93.5 0.413 -- 2.5 4.1 --

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 20.0 0.0 0.0 8500 8429 815 99.2 0.216 0.216 0.22 0.249 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 2.59 784 70 714 0.328 0.331 0.04 93.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model individual isotropic
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 6.08
c_scbond_it 3.9
c_mcangle_it 4.03
c_mcbond_it 2.41
c_improper_angle_d 1.85
c_dihedral_angle_d 25.8
c_angle_deg 2.0
c_bond_d 0.015
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.33
Luzzati Sigma A (Observed) 0.46
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.37
Luzzati Sigma A (R-Free Set) 0.5
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 871
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 22

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
EPMR Structure Solution
CNS 0.9 Structure Refinement
Software
Software Name Purpose
CNS version: 0.9 refinement
EPMR model building
SCALEPACK data reduction
DENZO data collection