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. IN THE WELL BUFFER: 20% W/V PEG 400 IN 0.1M HEPES-NAOH, PH 7.5 WITH 0.2M CALCIUM CHLORIDE. THE PROTEIN AT 15MG/ML, WITH 29MM NAD+.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 130.3 α = 90
b = 44.4 β = 106.7
c = 92.8 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 1997-12-15
Diffraction Radiation
Monochromator Protocol
GRAPHITE(002) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH2R -- -- --

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
2.54 30 95.1 -- 0.086 -- 3.2 -- 15753 -- -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)
2.54 2.59 85.6 -- 0.259 3.3 -- --

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 2.54 24.2 -- 0.0 -- 15750 758 95.1 -- 0.222 0.222 0.299 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 2.54 2.63 -- 49 853 0.387 0.479 -- 85.6
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.8
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 0.94
x_mcbond_it 3.4
x_dihedral_angle_d 22.3
x_angle_deg 1.23
x_mcangle_it 4.97
x_scangle_it 4.97
x_scbond_it 3.4
x_bond_d 0.006
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.45
Luzzati Resolution Cutoff (Low) 24.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3840
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 68

Software

Software
Software Name Purpose
X-PLOR refinement version: 3.851
DENZO data reduction
SCALEPACK data scaling
X-PLOR phasing version: 3.851