X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 292.0
Details PEG4000, t-butanol, sodium cacodylate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.49 α = 90
b = 55.26 β = 99.48
c = 111.73 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1998-07-09
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 -- SSRL BL9-1

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
3 50 97.5 0.104 -- -- 2.9 16915 16915 0.0 0.0 56.0
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)
3.0 3.16 98.4 0.262 -- 2.7 2.9 2478

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
-- 3.0 50.0 0.0 0.2 16915 16915 654 97.5 0.228 0.228 0.225 0.295 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 3.0 3.19 -- 93 2745 0.35 0.361 0.037 98.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 49.2
Anisotropic B[1][1] 3.62
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 3.49
Anisotropic B[2][2] -4.9
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.27
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 4.5
x_scbond_it 3.2
x_mcangle_it 5.3
x_mcbond_it 3.3
x_improper_angle_d 0.8
x_dihedral_angle_d 26.3
x_angle_deg 2.0
x_bond_d 0.012
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.37
Luzzati Sigma A (Observed) 0.55
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.52
Luzzati Sigma A (R-Free Set) 0.68
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5768
Nucleic Acid Atoms 0
Heterogen Atoms 145
Solvent Atoms 4

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (TRUNCATE) Data Reduction (data scaling)
AMORE Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
AMORE model building
TRUNCATE data reduction
MOSFLM data collection