X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details 10mg/mL PurR, 83 mM HEPES, pH 7.0, 5% PEG8000, 450 mM Lithium sulfate, 50 mM ammonium sulfate, 300 mM NaCl, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.00

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.08 α = 84.75
b = 72.16 β = 84.03
c = 82.97 γ = 67.47
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1997-09-01
IMAGE PLATE RIGAKU RAXIS IIC -- 1997-09-01
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.9790, 0.9788, 1.5418 ESRF ID14-1

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 20 97.6 -- 0.073 -- 4.3 -- 66722 -- 2.0 45.3
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)
2.0 2.28 96.6 -- 0.194 3.6 1.0 --

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
MAD 2.2 20.0 -- 0.0 -- 66365 3335 94.4 -- 0.1 0.188 0.237 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 2.2 2.34 -- 515 9938 0.233 0.308 0.014 89.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 52.7
Anisotropic B[1][1] 1.35
Anisotropic B[1][2] 2.47
Anisotropic B[1][3] -0.65
Anisotropic B[2][2] 0.88
Anisotropic B[2][3] 0.16
Anisotropic B[3][3] -2.23
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 23.5
c_mcangle_it 6.0
c_scbond_it 7.8
c_mcbond_it 4.39
c_improper_angle_d 0.93
c_scangle_it 9.74
c_bond_d 0.01
c_angle_deg 1.5
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.24
Luzzati Sigma A (Observed) 0.21
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.32
Luzzati Sigma A (R-Free Set) 0.3
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8383
Nucleic Acid Atoms 0
Heterogen Atoms 181
Solvent Atoms 568

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
MLPHARE phasing
CNS refinement version: 1.1