X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 293.0
Details 1.2M ammonium sulfate, 15%(w/v) glycerol, 0.1M HEPES, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 100.73 α = 90
b = 100.73 β = 90
c = 54.17 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD mirror 2008-04-22
Diffraction Radiation
Monochromator Protocol
Si SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0000 SPring-8 BL26B1

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
1.9 100 94.2 0.053 -- -- -- -- 16054 1.0 -- --
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)
1.9 1.93 100.0 0.129 -- -- -- --

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 1.9 20.0 -- -- -- 15236 804 99.78 -- 0.18311 0.18002 0.24462 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 1.902 1.951 -- 65 1109 0.215 0.314 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.296
Anisotropic B[1][1] -0.5
Anisotropic B[1][2] -0.25
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.5
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.75
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 20.903
r_mcangle_it 1.824
r_scbond_it 2.958
r_bond_refined_d 0.017
r_mcbond_it 1.097
r_dihedral_angle_3_deg 16.501
r_nbtor_refined 0.308
r_gen_planes_refined 0.006
r_chiral_restr 0.121
r_nbd_refined 0.224
r_xyhbond_nbd_refined 0.2
r_scangle_it 4.739
r_dihedral_angle_1_deg 6.347
r_angle_refined_deg 1.718
r_symmetry_hbond_refined 0.289
r_dihedral_angle_2_deg 29.095
r_symmetry_vdw_refined 0.239
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1673
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 161

Software

Software
Software Name Purpose
AMoRE phasing
REFMAC refinement version: 5.2.0019
HKL-2000 data reduction
HKL-2000 data scaling