X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6
Details PROTEIN CRYSTALLIZED IN 1.4M AMMONIUM SULFATE, 100MM MES PH6, 2% PEG 2000, 25MM MAGNESIUM ACETATE 2MM BETA-MERCAPTOETHANOL, pH 6.00

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.22 α = 90
b = 76.22 β = 90
c = 134.26 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH TOROIDAL MIRROR 2000-09-18
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID09 -- ESRF ID09

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
1.6 25.2 99.1 -- 0.076 -- 8.2 -- 30736 -- -- 20.4
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)
1.6 1.69 99.1 -- 0.282 4.3 8.2 --

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
OTHER 1.6 25.19 -- 0.0 -- 30664 1568 98.2 -- 0.193 0.193 0.21 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 1.6 1.7 -- 280 4697 0.231 0.259 0.015 98.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 22.9
Anisotropic B[1][1] 0.67
Anisotropic B[1][2] 0.32
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.67
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.35
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.56
c_scbond_it 2.72
c_mcangle_it 2.51
c_mcbond_it 1.87
c_improper_angle_d 0.9
c_bond_d 0.004
c_angle_deg 1.1
c_dihedral_angle_d 20.9
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.18
Luzzati Sigma A (Observed) 0.13
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.21
Luzzati Sigma A (R-Free Set) 0.15
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1534
Nucleic Acid Atoms 0
Heterogen Atoms 49
Solvent Atoms 264

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (SCALA, TRUNCATE) Data Reduction (data scaling)
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement