X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 293.0
Details PEG8000, cacodylate, CaCl2, glycerol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 141.87 α = 90
b = 141.87 β = 90
c = 120.96 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2002-04-08
Diffraction Radiation
Monochromator Protocol
120 degree plus inversion 120 degree collection MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --
SYNCHROTRON CHESS BEAMLINE F2 0.94 CHESS F2
SYNCHROTRON APS BEAMLINE 19-BM 0.94 APS 19-BM

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
3.1 40 0.99 -- 0.08 -- 9.0 -- 24919 2.0 2.0 --
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)
3.1 3.15 0.99 -- 0.54 -- -- --

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 3.1 40.0 -- 2.0 -- 21348 1072 84.8 -- 0.244 0.251 0.283 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 3.1 3.29 -- 135 2448 0.322 0.348 0.03 62.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 71.3
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
x_dihedral_angle_d 25.3
x_mcangle_it 5.79
x_scangle_it 7.3
x_angle_deg 2.4
x_improper_angle_d 2.2
x_bond_d 0.023
x_scbond_it 4.57
x_mcbond_it 3.32
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.42
Luzzati Sigma A (Observed) 0.61
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.48
Luzzati Sigma A (R-Free Set) 0.64
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7475
Nucleic Acid Atoms 0
Heterogen Atoms 118
Solvent Atoms 78

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
SCALEPACK data reduction
X-PLOR(ONLINE) version: 3.851 refinement
HKL-2000 data collection
CNS model building