X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 9
Details PROTEIN SOLUTION (4MG/ML IN 20MM TRIS-HCL PH 7.5, 50MM NACL) WAS INCUBATED WITH 5MM INHIBITOR FOR 30MINS PRIOR TO SETTING UP CRYSTALLISATION TRIALS. THE CRYSTALLISATION DROPS CONTAINED A 1:1 MIXTURE OF COMPLEX SOLUTION AND RESERVOIR BUFFER (2.6 - 2.8 M NACL, 0.1 M HEPES PH 9.0).

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.52 α = 90
b = 56.52 β = 90
c = 263.76 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC SILICON MIRROR 2000-08-22
Diffraction Radiation
Monochromator Protocol
SI(III) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX9.6 -- SRS PX9.6

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
2.1 36.3 70.0 0.147 0.147 -- 2.7 -- 18276 -- -- 14.1
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)
2.1 2.27 40.0 0.385 0.385 2.5 1.7 --

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 2.1 36.3 -- 0.0 -- 18276 1439 69.9 -- -- 0.212 0.256 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 2.1 2.18 -- 52 696 0.266 0.288 0.04 29.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 22.0
Anisotropic B[1][1] -4.81
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.81
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 9.61
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.83
c_bond_d 0.006
c_scangle_it 1.78
c_mcbond_it 0.88
c_dihedral_angle_d 23.0
c_mcangle_it 1.14
c_scbond_it 1.49
c_angle_deg 1.1
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.27
Luzzati Sigma A (Observed) 0.24
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.32
Luzzati Sigma A (R-Free Set) 0.25
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2504
Nucleic Acid Atoms 0
Heterogen Atoms 56
Solvent Atoms 184

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
AMORE Structure Solution
CNX 2000 Structure Refinement
Software
Software Name Purpose
CNX version: 2000 refinement
AMORE model building