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 AND COMPLEXED WITH NITRITE BY SOAKING IN 10 MM BENZYL VIOLOGEN AND 30 MM SODIUM NITRITE FOR 30 MINUTES., vapor diffusion - hanging drop in anaerobic atmosphere

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 146.8 α = 90
b = 146.8 β = 90
c = 81.8 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 1995-12
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
2.9 50 97.7 0.09 -- -- 4.7 -- 19946 -- 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)
2.9 3.0 99.0 0.29 -- 6.9 -- --

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 OXIDIZED FDH-H (PDB ENTRY 1FDO) 2.9 6.0 -- 2.0 -- 16240 732 91.3 -- 0.192 0.192 0.284 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 2.9 2.99 -- 60 1488 0.223 0.326 0.04 88.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 25.8
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 1.66
x_bond_d 0.014
x_angle_deg 1.92
x_dihedral_angle_d 25.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5575
Nucleic Acid Atoms 0
Heterogen Atoms 106
Solvent Atoms 62

Software

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