X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop in Anaerobic Atmosphere
pH 7.5
Details FDH-H WAS CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION IN AN ANAEROBIC ATMOSPHERE IN THE PRESENCE OF 1.5 M AMMONIUM SULFATE, 1% PEG 400, 20 MM SODIUM FORMATE AND 100 MM HEPES/NAOH AT PH 7.5. PRIOR TO FREEZING IN LIQUID NITROGEN, CRYSTALS WERE OXIDIZED BY SOAKING IN 10 MM BENZYL VIOLOGEN FOR 30 MINUTES., vapor diffusion - hanging drop in anaerobic atmosphere

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 146.6 α = 90
b = 146.6 β = 90
c = 81.1 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS MIRRORS 1995-10
Diffraction Radiation
Monochromator Protocol
NI FILTER --
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
2.8 50 93.4 0.079 -- -- 4.0 -- 20861 -- 1.0 --
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)
2.8 2.9 91.4 0.2 -- 8.4 -- --

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
DIFFERENCE FOURIER ANALYSIS USING PHASES FROM THE STRUCTURE OF REDUCED FDH-H (PDB ENTRY 1AA6) 2.8 6.0 -- 2.0 -- 18013 849 90.0 -- 0.192 0.192 0.281 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 2.8 2.89 -- 69 1518 0.231 0.33 0.039 77.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 23.5
RMS Deviations
Key Refinement Restraint Deviation
x_dihedral_angle_d 24.7
x_improper_angle_d 1.54
x_angle_deg 1.85
x_bond_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5575
Nucleic Acid Atoms 0
Heterogen Atoms 103
Solvent Atoms 64

Software

Software
Software Name Purpose
X-PLOR model building version: 3.1
X-PLOR refinement version: 3.1
DENZO data reduction
SCALEPACK data scaling
X-PLOR phasing version: 3.1