X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.8
Details HANGING DROP VAPOUR DIFFUSION, 2+2 MICROLITER DROPS. THE PROTEIN AT 5MG/ML IN 100MM TRIS-HCL AT PH 7.5 WITH 12.5MM NAD+. DROPS EQUILIBRIATED AGAINST 1.7M UNBUFFERED AMMONIUM SULFATE.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 136.7 α = 90
b = 136.7 β = 90
c = 121.2 γ = 120
Symmetry
Space Group P 62 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MIRRORS 1994-11-15
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

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 21 94.1 -- 0.113 -- 4.6 -- 24865 -- -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)
2.4 2.53 93.0 -- 0.418 3.7 5.2 --

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
MOLECULAR REPLACEMENT 2.4 21.0 -- 0.0 -- 24864 2002 94.1 -- 0.19 0.19 0.236 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 2.4 2.49 -- 206 2180 0.283 0.356 -- 88.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.8
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 3.88
x_scbond_it 2.77
x_mcangle_it 3.88
x_mcbond_it 2.77
x_improper_angle_d 0.97
x_bond_d 0.006
x_angle_deg 1.272
x_dihedral_angle_d 22.73
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.38
Luzzati Resolution Cutoff (Low) 21.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3837
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 139

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
X-PLOR 3.1 Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
X-PLOR version: 3.1 model building