X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details HANGING DROP VAPOUR DIFFUSION, 2+2 MICROLITER DROPS. THE WELL BUFFER: 20% V/V PEG 400 IN 0.1M HEPES-NAOH, PH 7.5 WITH 0.2M CALCIUM CHLORIDE. THE PROTEIN AT 10MG/ML IN 100MM TRIS-HCL WITH 12.5MM NAD+.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 129.33 α = 90
b = 44.28 β = 105.39
c = 91.17 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MIRRORS 1995-11-12
Diffraction Radiation
Monochromator Protocol
SI CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX9.6 -- SRS PX9.6

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
2.2 25 96.4 -- 0.081 -- 2.3 -- 24710 -- -3.0 --
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)
2.2 2.28 85.2 -- 0.298 2.9 2.0 --

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 2.2 25.0 -- 0.0 -- 24710 1198 96.4 -- 0.206 0.206 0.282 RANDOM, USING XPLOR
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 2.2 2.28 -- 105 2043 0.317 0.34 -- 85.2
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.3
RMS Deviations
Key Refinement Restraint Deviation
x_dihedral_angle_d 22.46
x_scbond_it 3.27
x_scangle_it 4.52
x_bond_d 0.005
x_angle_deg 1.235
x_mcbond_it 3.27
x_mcangle_it 4.52
x_improper_angle_d 0.95
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.38
Luzzati Resolution Cutoff (Low) 25.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3840
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 188

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE, CCP4 (TFFC) Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
CCP4 version: (TFFC) model building
X-PLOR version: 3.851 refinement
AMORE model building