X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 288.0
Details 25% PEG3350, 0.1 M Ammonium Sulphate and 0.1 M Bis-Tris, 2.5 mM dcAdoMet, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 196.3 α = 90
b = 134.18 β = 94.38
c = 48.32 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm mirrors 2006-12-06
Diffraction Radiation
Monochromator Protocol
Bent silicon crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I911-2 1.043 MAX II I911-2

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 20 96.1 0.72 0.115 -- 3.22 -- 80780 2.0 2.0 30.07
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)
2.0 2.051 100.0 0.269 29.3 5.25 3.22 38389

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 2.0 19.99 -- -- -- 79372 4178 100.0 0.18217 0.18217 0.18048 0.21407 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 2.0 2.051 -- 305 5793 0.25 0.304 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.935
Anisotropic B[1][1] 1.85
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -2.02
Anisotropic B[2][2] -2.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.06
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.125
r_nbtor_refined 0.303
r_mcbond_it 0.823
r_dihedral_angle_3_deg 14.351
r_dihedral_angle_4_deg 17.677
r_nbd_refined 0.205
r_scbond_it 2.006
r_symmetry_hbond_refined 0.266
r_mcangle_it 1.358
r_symmetry_vdw_refined 0.201
r_dihedral_angle_1_deg 6.098
r_bond_refined_d 0.012
r_xyhbond_nbd_refined 0.158
r_angle_refined_deg 1.302
r_chiral_restr 0.091
r_gen_planes_refined 0.005
r_dihedral_angle_2_deg 37.799
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6753
Nucleic Acid Atoms 0
Heterogen Atoms 124
Solvent Atoms 403

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
REFMAC refinement version: 5.2.0019
REFMAC refinement version: 5.2.0019
REFMAC refinement version: 5.2.0019
MAR345dtb data collection
XDS data reduction
XSCALE data scaling
PHASER phasing