X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details 1.2M AMMONIUM SULPHATE, 4% PEG400, 0.1M HEPES PH7.5 ARGON ATMOSPHERE, 28MG/ML PROTEIN WITH 1MM FE(II), 10MM N-(CARBOXYCARBONYL)-D-PHENYLALANINE, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.85 α = 90
b = 86.85 β = 90
c = 150.52 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2004-11-10
Diffraction Radiation
Monochromator Protocol
double crystal Si(III) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX10.1 1.488 SRS PX10.1

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
2.7 43.45 99.9 0.082 -- -- 7.1 16510 16510 -- -- 53.0
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)
2.7 2.8 100.0 0.446 -- 4.9 7.1 1619

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 1H2N 2.7 43.45 -- 0.0 15709 15709 1589 95.3 -- 0.21 0.21 0.244 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 2.7 2.8 -- 137 1263 0.356 0.416 0.036 86.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 58.3
Anisotropic B[1][1] -6.89
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -6.89
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 13.79
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.07
c_scbond_it 1.88
c_mcangle_it 2.25
c_mcbond_it 1.27
c_improper_angle_d 0.75
c_bond_d 0.01
c_angle_deg 1.2
c_dihedral_angle_d 24.1
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.33
Luzzati Sigma A (Observed) 0.35
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.41
Luzzati Sigma A (R-Free Set) 0.42
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2715
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 90

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
SCALEPACK data reduction
DENZO data collection