X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.1
Temperature 277.0
Details 1M NaOAc, 0.1M Imidazole

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 98 α = 90
b = 98 β = 90
c = 80.6 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX300HE -- 2014-11-22
Diffraction Radiation
Monochromator Protocol
Main beamline optics is a double-crystal monochromator and a horizontal focusing mirror. SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU

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
2.04 50 100.0 0.068 -- 25.066 5.7 -- 28099 -- -- 23.37
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)
2.04 2.11 100.0 -- -- 2.1 5.7 --

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 2.04 42.435 -- -- -- 25569 1344 95.83 -- 0.20152 0.20026 0.22574 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 2.04 2.093 -- 62 1142 0.239 0.239 -- 58.39
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.325
Anisotropic B[1][1] 0.26
Anisotropic B[1][2] 0.13
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.26
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.85
RMS Deviations
Key Refinement Restraint Deviation
r_long_range_B_other 5.231
r_chiral_restr 0.096
r_dihedral_angle_4_deg 18.752
r_mcangle_other 2.902
r_dihedral_angle_3_deg 14.539
r_long_range_B_refined 5.231
r_mcangle_it 2.902
r_gen_planes_other 0.026
r_gen_planes_refined 0.015
r_scbond_it 2.111
r_mcbond_other 1.778
r_scangle_other 3.503
r_bond_refined_d 0.01
r_bond_other_d 0.0
r_mcbond_it 1.782
r_dihedral_angle_2_deg 35.834
r_angle_refined_deg 1.346
r_angle_other_deg 3.543
r_dihedral_angle_1_deg 5.519
r_scbond_other 2.11
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2224
Nucleic Acid Atoms 0
Heterogen Atoms 22
Solvent Atoms 65

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0049
Coot model building version: 0.7.2
HKL-2000 data processing