X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop Nanodrop
pH 7
Temperature 277.0
Details 0.2M MgCl2, 2.5M NaCl, 0.1M Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.47 α = 90
b = 93.47 β = 90
c = 101.16 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD Adjustable focusing mirrors. K-B geometry 2005-08-03
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL SI (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-D 0.97942 APS 23-ID-D

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
2.25 29.29 100.0 0.13 0.13 -- 14.9 -- 8245 -- -- --
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)
2.25 2.31 -- 0.976 0.976 0.7 15.3 --

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
SAD 2.25 29.29 -- -- -- 7863 382 99.92 0.177 -- 0.175 0.217 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 2.251 2.31 -- 31 566 0.208 0.215 -- 99.83
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 49.769
Anisotropic B[1][1] -1.34
Anisotropic B[1][2] -0.67
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.34
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.01
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.07
r_chiral_restr 0.069
r_xyhbond_nbd_refined 0.181
r_mcbond_it 2.202
r_dihedral_angle_3_deg 16.083
r_symmetry_vdw_other 0.245
r_nbd_refined 0.229
r_symmetry_vdw_refined 0.205
r_gen_planes_refined 0.005
r_nbtor_refined 0.19
r_scbond_it 6.736
r_mcangle_it 3.196
r_bond_refined_d 0.015
r_angle_other_deg 0.804
r_scangle_it 8.205
r_bond_other_d 0.001
r_angle_refined_deg 1.357
r_gen_planes_other 0.001
r_dihedral_angle_4_deg 9.441
r_nbtor_other 0.088
r_mcbond_other 0.53
r_dihedral_angle_2_deg 36.348
r_nbd_other 0.174
r_symmetry_hbond_refined 0.274
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 949
Nucleic Acid Atoms 0
Heterogen Atoms 8
Solvent Atoms 55

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
SCALA data scaling
PDB_EXTRACT data extraction version: 1.601
MOSFLM data reduction
CCP4 data scaling version: (SCALA)
SHELXD phasing
autoSHARP phasing