X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Batch
pH 7.5
Temperature 285.0
Details Tris/HCl, hexylene glycol, Ammonium Sulfate, pH 7.5, Batch, temperature 285K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 121.63 α = 90
b = 121.63 β = 90
c = 108.75 γ = 90
Symmetry
Space Group I 4 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2000-02-05
Diffraction Radiation
Monochromator Protocol
Si SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.0 PHOTON FACTORY BL-6A

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
1.94 28.67 93.5 0.064 -- -- -- 28896 28532 0.0 3.0 --
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)
1.94 2.04 93.5 -- -- -- -- --

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
MOLECULAR REPLACEMENT 1.95 84.51 -- 0.0 28531 27080 1451 94.42 -- 0.1619 0.16076 0.1833 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 1.945 1.995 -- 36 656 0.366 0.385 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.174
Anisotropic B[1][1] -0.11
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.11
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.22
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.2
r_nbd_refined 0.198
r_gen_planes_other 0.002
r_gen_planes_refined 0.005
r_chiral_restr 0.077
r_dihedral_angle_3_deg 16.547
r_dihedral_angle_1_deg 3.663
r_angle_other_deg 0.721
r_angle_refined_deg 1.279
r_bond_other_d 0.001
r_bond_refined_d 0.009
r_xyhbond_nbd_refined 0.133
r_xyhbond_nbd_other 0.008
r_symmetry_vdw_refined 0.092
r_symmetry_vdw_other 0.223
r_symmetry_hbond_refined 0.931
r_mcbond_it 0.604
r_mcangle_it 1.135
r_scbond_it 1.709
r_scangle_it 2.835
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2229
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 190

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
AMoRE model building
SCALA data reduction
MOSFLM data collection