X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 10% Ethanol, 0.1 M Tris, 0.3 M magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 36.31 α = 90
b = 74.26 β = 90
c = 106.46 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 MARMOSAIC 300 mm CCD mirrors 2009-07-07
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 1.5418 APS 21-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
2.5 18.6 99.7 -- 0.068 -- 6.0 10002 10002 2.0 2.0 --
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)
2.5 2.56 100.0 0.102 0.19 -- 6.3 --

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
MOLECULAR REPLACEMENT 2.5 18.58 -- -- 10002 10002 502 99.6 -- 0.2233 0.22021 0.28637 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 2.5 2.561 -- 31 711 0.267 0.396 -- 99.07
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.63
Anisotropic B[1][1] 0.19
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.15
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.04
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.009
r_mcangle_it 1.081
r_nbtor_other 0.09
r_angle_other_deg 1.3
r_symmetry_vdw_refined 0.117
r_mcbond_other 0.085
r_nbd_other 0.193
r_chiral_restr 0.171
r_gen_planes_other 0.001
r_symmetry_hbond_refined 0.187
r_nbd_refined 0.208
r_scbond_it 1.189
r_bond_other_d 0.002
r_xyhbond_nbd_refined 0.146
r_dihedral_angle_2_deg 38.183
r_scangle_it 1.87
r_dihedral_angle_1_deg 9.547
r_gen_planes_refined 0.004
r_nbtor_refined 0.192
r_dihedral_angle_3_deg 18.891
r_angle_refined_deg 1.405
r_mcbond_it 0.626
r_symmetry_vdw_other 0.22
r_dihedral_angle_4_deg 20.479
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2238
Nucleic Acid Atoms 0
Heterogen Atoms 23
Solvent Atoms 88

Software

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