X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6.4
Details 0.1 M MES/NAOH, PH 6.4, 200 MM magnesium acetate and 20% (W/V) PEG 8000; for cryoprotection 16% glycerol was added to the reservoir buffer, VAPOR DIFFUSION

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.75 α = 90
b = 125.2 β = 90.37
c = 89.25 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 BENT MIRRORS 2010-12-05
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02

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
2.75 30 99.3 0.034 0.034 -- 3.7 -- 36793 -- -- --
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)
2.75 2.82 100.0 0.324 0.324 2.4 3.8 --

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 2.75 28.94 -- -- -- 34888 1882 99.35 -- 0.20317 0.20099 0.24192 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 2.75 2.821 -- 126 2627 0.348 0.373 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 63.656
Anisotropic B[1][1] -0.35
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.55
Anisotropic B[2][2] 2.52
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.15
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_other 0.201
r_chiral_restr 0.077
r_angle_other_deg 4.18
r_gen_planes_other 0.005
r_xyhbond_nbd_refined 0.176
r_angle_refined_deg 1.508
r_nbd_other 0.233
r_dihedral_angle_4_deg 13.865
r_metal_ion_refined 0.042
r_gen_planes_refined 0.005
r_scangle_it 2.093
r_bond_refined_d 0.012
r_dihedral_angle_2_deg 36.596
r_mcangle_it 0.899
r_dihedral_angle_3_deg 16.22
r_nbtor_other 0.118
r_dihedral_angle_1_deg 6.25
r_nbd_refined 0.214
r_scbond_it 1.258
r_symmetry_vdw_refined 0.234
r_symmetry_hbond_refined 0.173
r_bond_other_d 0.0
r_xyhbond_nbd_other 0.066
r_nbtor_refined 0.18
r_mcbond_it 0.471
r_mcbond_other 0.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7964
Nucleic Acid Atoms 0
Heterogen Atoms 129
Solvent Atoms 344

Software

Software
Software Name Purpose
MOLREP phasing
REFMAC refinement version: 5.2.0019
XDS data reduction
SCALA data scaling