X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 290.0
Details 2M (NH4)2SO4, 1% glycerol, 0.1 M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 110.05 α = 90
b = 109.57 β = 90
c = 45.3 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1999-04-04
Diffraction Radiation
Monochromator Protocol
Cyclindrically bent triangular Si(111) asymmetric cut, horizontal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 1.08 SSRL BL7-1

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
2.35 19.8 94.9 -- 0.08 -- 2.76 -- 22313 -- -3.0 32.7
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)
2.35 2.43 92.0 -- 0.423 1.86 2.38 2120

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 2.35 19.8 -- 0.0 -- 21660 2156 97.16 -- 0.24935 0.2473 0.26803 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 2.35 2.412 -- 135 1280 0.36 0.348 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.686
Anisotropic B[1][1] -1.12
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.96
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.85
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.252
r_nbd_refined 0.249
r_gen_planes_other 0.002
r_gen_planes_refined 0.005
r_chiral_restr 0.083
r_dihedral_angle_3_deg 18.483
r_dihedral_angle_1_deg 3.077
r_angle_other_deg 0.783
r_angle_refined_deg 1.463
r_bond_other_d 0.001
r_bond_refined_d 0.009
r_xyhbond_nbd_refined 0.176
r_xyhbond_nbd_other 0.217
r_symmetry_vdw_refined 0.192
r_symmetry_vdw_other 0.249
r_symmetry_hbond_refined 0.751
r_mcbond_it 0.319
r_mcangle_it 0.614
r_scbond_it 1.126
r_scangle_it 1.978
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3149
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 144

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
AMoRE model building
SCALEPACK data reduction
DENZO data collection