X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Hanging Drop Vapor Diffusion Method
pH 7
Temperature 277.0
Details PLATE-SHAPED CRYSTALS WERE INFREQUENTLY GROWN BY HANGING DROP VAPOR DIFFUSION METHOD. RESERVOIR SOLUTION CONTAINED 0.050M KCL, 0.01M MGCL2, 0.05M SODIUM CACODYLATE, PH 7.0, 10% PEG 3350, and 20% (V/V) ETHYLENE GLYCOL. THE DROP CONTAINED 1:1 MIXTURE OF RESERVOIR SOLUTION AND PROTEIN (10-15 MG/ML), HANGING DROP VAPOR DIFFUSION METHOD, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.75 α = 67.47
b = 66.37 β = 78.61
c = 76.67 γ = 90.18
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X9B -- NSLS X9B

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
2.53 15 87.6 0.036 -- -- 1.8 -- 28842 -- 0.04 25.0
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)
2.53 2.62 75.7 0.096 -- 5.4 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
MOLECULAR REPLACEMENT 2.53 15.0 -- 0.2 -- 27399 1443 87.6 -- 0.216 0.216 0.279 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 2.53 2.62 -- 140 2332 0.286 0.347 -- 75.7
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.5
Anisotropic B[1][1] 1.355
Anisotropic B[1][2] -2.813
Anisotropic B[1][3] 3.866
Anisotropic B[2][2] -0.276
Anisotropic B[2][3] 5.223
Anisotropic B[3][3] -1.08
RMS Deviations
Key Refinement Restraint Deviation
x_scbond_it 2.669
x_mcbond_it 1.675
x_improper_angle_d 0.82
x_bond_d 0.007
x_angle_deg 1.22
x_dihedral_angle_d 23.0
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.31
Luzzati Sigma A (Observed) 0.28
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.41
Luzzati Sigma A (R-Free Set) 0.36
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6893
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 141

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS, X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
CNS refinement
AMORE model building