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 = 131.9 α = 90
b = 45.2 β = 107.1
c = 93.5 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MIRRORS 1995-05-11
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 20 88.9 -- 0.101 -- 2.7 -- 16682 -- -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 2.6 81.7 -- 0.48 1.6 2.2 --

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 2.5 20.0 -- 0.0 -- 16513 810 89.1 -- 0.213 0.213 0.292 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 2.5 2.56 -- 46 904 0.322 0.366 -- 78.3
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.0
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 5.45
x_angle_deg 1.257
x_scbond_it 3.77
x_bond_d 0.006
x_mcbond_it 3.77
x_dihedral_angle_d 22.93
x_mcangle_it 5.45
x_improper_angle_d 1.07
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.38
Luzzati Resolution Cutoff (Low) 20.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3840
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 61

Software

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