X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop Microseeding
pH 6.15
Temperature 277.0
Details FROM 2.15 M (NH4)2SO4, 55 MG/ML PROTEIN, 4 DEG C, PH 6.15, HANGING DROP, MICROSEED FROM NATIVE FE-SOD OF P.SHERM., SOAKED FOR 24 H IN 150 MM SODIUM AZIDE, vapor diffusion - hanging drop - microseeding, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.68 α = 90
b = 85.42 β = 90
c = 108.76 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 295
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR SIEMENS -- 1997-03
Diffraction Radiation
Monochromator Protocol
GRAPHITE(002) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE ENRAF-NONIUS FR591 -- -- --

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
1.55 39.8 84.6 0.044 0.044 -- 3.8 -- 45471 -- 2.0 14.0
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)
1.55 1.6 61.9 0.158 0.158 4.8 1.6 --

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
ISOMORPHOUS WITH FE-SOD OF P.SHERMANII 1.55 8.0 -- 4.5 -- 42899 4318 80.0 -- 0.171 0.171 0.198 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 1.55 1.62 -- 332 2995 0.217 0.22 -- 50.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 15.4
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 2.5
x_scbond_it 2.0
x_mcangle_it 2.0
x_mcbond_it 1.5
x_improper_angle_d 0.98
x_bond_d 0.005
x_angle_deg 1.42
x_dihedral_angle_d 21.35
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.16
Luzzati Resolution Cutoff (Low) 5.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3208
Nucleic Acid Atoms 0
Heterogen Atoms 8
Solvent Atoms 424

Software

Computing
Computing Package Purpose
SAINT Data Reduction (intensity integration)
SAINT, CCP4 (AGROVATA, SCALA, TRUNCATE) 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