X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 282.0
Details PEG 4000, ethylene glycol, sodium chloride, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 282K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.1 α = 90
b = 93.1 β = 90
c = 421.8 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Bent Conical SI Mirror (RH Coating) 1999-05-01
Diffraction Radiation
Monochromator Protocol
Bent Cylindrical GE (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 1.0000 APS 14-BM-C

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
1.86 20 99.1 0.065 -- -- 9.8 92896 92060 0.0 -3.0 21.1
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)
1.86 1.93 95.6 0.54 -- 2.2 6.3 8678

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 1.86 20.0 -3.0 0.0 92052 91188 9022 99.1 0.232 0.232 0.23 0.246 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 1.86 1.98 -- 1419 13009 0.3212 0.333 0.0088 96.05
X Ray Diffraction 1.98 2.13 -- 1455 -- 0.2775 0.294 0.0077 98.46
X Ray Diffraction 2.13 2.34 -- 1485 -- 0.2663 0.2871 0.0075 99.89
X Ray Diffraction 2.34 2.68 -- 1501 -- 0.248 0.2768 0.0071 99.98
X Ray Diffraction 2.68 3.38 -- 1575 -- 0.2254 0.2433 0.0061 99.98
X Ray Diffraction 3.38 20.0 -- 1587 -- 0.2025 0.2143 0.0054 99.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 36.2
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
c_mcbond_it 1.39
c_dihedral_angle_d 26.1
c_angle_deg 1.3
c_improper_angle_d 1.25
c_scbond_it 1.67
c_mcangle_it 2.18
c_scangle_it 2.46
c_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.26
Luzzati Sigma A (Observed) 0.28
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.29
Luzzati Sigma A (R-Free Set) 0.28
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5438
Nucleic Acid Atoms 759
Heterogen Atoms 5
Solvent Atoms 503

Software

Software
Software Name Purpose
CNS refinement
DENZO data reduction
SCALEPACK data scaling
CNS phasing