X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 1.5M Li sulfate, 0.1M Na HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 101.99 α = 90
b = 150.74 β = 90
c = 167.07 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-06-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6B 0.978 PHOTON FACTORY BL-6B

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
1.8 40 99.9 0.063 -- -- 5.5 -- 237380 -- -- 22.1
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)
1.8 1.9 99.5 0.331 -- -- 4.5 --

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
SIRAS 1.8 40.0 -- -- -- 225343 11908 99.9 -- 0.17592 0.175 0.1932 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 1.8 1.847 -- 882 16314 0.242 0.275 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.765
Anisotropic B[1][1] 0.67
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.67
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.199
r_nbd_refined 0.224
r_gen_planes_other 0.002
r_gen_planes_refined 0.005
r_chiral_restr 0.07
r_dihedral_angle_2_deg 18.121
r_dihedral_angle_1_deg 3.956
r_angle_other_deg 0.727
r_angle_refined_deg 1.232
r_bond_other_d 0.001
r_bond_refined_d 0.009
r_xyhbond_nbd_refined 0.155
r_xyhbond_nbd_other 0.354
r_symmetry_vdw_refined 0.254
r_symmetry_vdw_other 0.291
r_symmetry_hbond_refined 0.242
r_mcbond_it 0.591
r_mcangle_it 1.122
r_scbond_it 1.68
r_scangle_it 2.815
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11928
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 1396

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
MLPHARE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement