X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Details DIALYSIS OF PROTEIN AT 8.3 MG/ML IN 20MM TRIS HCL AT PH7.0, 10%(W/V) GLYCEROL, 150MM NACL, 10MM DTT, AND 0.1MM EDTA AGAINST 20MM IMIDAZOLE AT PH 6.5, 80MM NACL, AND 10MM DTT. DIALYSIS DONE AT ROOM TEMPERATURE.(ALL CONCENTRATIONS ARE IN MILLI-MOLAR)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.8 α = 90
b = 41.8 β = 90
c = 214.6 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate BENT MIRRORS 1998-07-27
Diffraction Radiation
Monochromator Protocol
SI(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X9B 0.9793,0.9789,0.9686 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
1.9 40 99.5 -- 6.1 -- 13.7 -- 16011 -- -3.0 17.3
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)
1.9 1.94 100.0 -- 18.4 -- -- --

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 1.9 40.0 -- 0.0 -- 15702 1588 98.1 -- -- 0.21 0.262 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 1.9 2.02 -- 248 2234 0.26 0.318 0.02 97.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 24.1
Anisotropic B[1][1] 4.27
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.27
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -8.54
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 4.79
c_scbond_it 3.58
c_mcangle_it 3.23
c_mcbond_it 2.2
c_improper_angle_d 0.91
c_bond_d 0.01
c_angle_deg 1.4
c_dihedral_angle_d 18.7
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Luzzati Sigma A (Observed) 0.2
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.3
Luzzati Sigma A (R-Free Set) 0.26
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1389
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 228

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE, PHASES V. 95 Structure Solution
CNS 0.4 Structure Refinement
Software
Software Name Purpose
CNS version: 0.4 refinement
PHASES-95 model building
SOLVE model building