X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.8
Temperature 277.0
Details 100mM Tris.HCl pH 7.7-7.8, 2mM sodium 4-(hydroxymercury)benzoate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.79 α = 90
b = 42.11 β = 104.4
c = 72.02 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 OXFORD SAPPHIRE CCD -- 2007-05-03
Diffraction Radiation
Monochromator Protocol
capillary SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.54 -- --

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
2.1 20 -- -- 0.042 -- 2.7 -- 13657 2.0 0.0 --
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)
2.1 2.2 -- -- 0.315 4.0 2.5 1951

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 2.1 10.32 -- -- -- 11970 645 87.78 -- 0.23135 0.22912 0.27182 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 2.1 2.154 -- 33 809 0.305 0.337 -- 83.12
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.361
Anisotropic B[1][1] 0.19
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.7
Anisotropic B[2][2] -0.61
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.77
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.523
r_angle_refined_deg 1.762
r_dihedral_angle_4_deg 14.17
r_nbd_refined 0.232
r_nbtor_refined 0.306
r_scbond_it 1.786
r_dihedral_angle_1_deg 7.401
r_gen_planes_refined 0.006
r_mcbond_it 0.625
r_bond_refined_d 0.013
r_mcangle_it 1.058
r_xyhbond_nbd_refined 0.216
r_chiral_restr 0.11
r_metal_ion_refined 0.18
r_symmetry_vdw_refined 0.247
r_dihedral_angle_3_deg 19.073
r_symmetry_hbond_refined 0.289
r_dihedral_angle_2_deg 37.996
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2039
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 131

Software

Software
Software Name Purpose
CrysalisPro data collection version: Oxford Diffraction2006
AMoRE phasing
REFMAC refinement version: 5.2.0019
CrysalisPro data reduction version: Oxford Diffraction2006
SCALEPACK data scaling