X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 277.0
Details 0.2000M MgCl2, 20.0000% PEG-8000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.83 α = 116.57
b = 70.92 β = 104.63
c = 77.19 γ = 102.32
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2008-01-23
Diffraction Radiation
Monochromator Protocol
Single crystal Si(111) bent monochromator (horizontal focusing) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 -- SSRL BL11-1

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
1.9 29.37 92.2 0.051 -- -- 7.86 -- 84662 -- -3.0 30.367
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)
1.9 1.97 63.7 0.649 -- 2.28 -- --

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
SAD 1.9 29.374 -- 0.0 -- 84658 4235 93.02 -- 0.189 0.187 0.229 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 1.899 1.948 -- 208 3974 0.269 0.355 -- 62.42
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.362
Anisotropic B[1][1] 2.03
Anisotropic B[1][2] 0.45
Anisotropic B[1][3] 1.72
Anisotropic B[2][2] -1.37
Anisotropic B[2][3] -0.17
Anisotropic B[3][3] 0.25
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.015
r_xyhbond_nbd_other 0.148
r_mcbond_other 0.647
r_gen_planes_refined 0.006
r_symmetry_hbond_refined 0.144
r_nbtor_other 0.089
r_nbd_refined 0.214
r_xyhbond_nbd_refined 0.154
r_nbd_other 0.195
r_mcbond_it 1.841
r_angle_other_deg 0.933
r_dihedral_angle_3_deg 11.583
r_mcangle_it 2.546
r_gen_planes_other 0.001
r_dihedral_angle_4_deg 17.391
r_chiral_restr 0.095
r_metal_ion_refined 0.103
r_scbond_it 4.681
r_symmetry_vdw_other 0.297
r_dihedral_angle_2_deg 35.668
r_bond_other_d 0.001
r_nbtor_refined 0.182
r_scangle_it 6.083
r_angle_refined_deg 1.587
r_dihedral_angle_1_deg 3.743
r_symmetry_vdw_refined 0.156
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7631
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 516

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PHENIX refinement
SOLVE phasing
MolProbity model building version: 3beta29
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.004
XDS data reduction