X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 292.0
Details 20% (w/v) PEG 4000, 0.2M MgCl2, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 175.07 α = 90
b = 175.07 β = 90
c = 70.62 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2008-05-25
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 1.0007 SLS X10SA

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
2.8 30 99.7 -- 0.069 -- 7.6 30693 30615 -- 5.0 53.0
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)
2.8 2.9 99.8 -- 0.335 5.9 7.6 30615

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 2.8 29.96 -- -- -- 29048 1544 99.77 -- 0.1553 0.15258 0.20692 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 2.8 2.872 -- 109 2108 0.234 0.296 -- 99.82
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 52.562
Anisotropic B[1][1] 0.75
Anisotropic B[1][2] 0.37
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.75
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.12
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 21.551
r_xyhbond_nbd_refined 0.159
r_angle_refined_deg 1.784
r_gen_planes_refined 0.006
r_bond_refined_d 0.019
r_dihedral_angle_2_deg 37.424
r_nbtor_other 0.112
r_nbtor_refined 0.2
r_mcbond_other 3.61
r_angle_other_deg 3.623
r_scbond_it 3.171
r_bond_other_d 0.0
r_dihedral_angle_3_deg 18.569
r_gen_planes_other 0.008
r_scangle_it 4.999
r_symmetry_hbond_refined 0.522
r_nbd_refined 0.236
r_dihedral_angle_1_deg 6.797
r_chiral_restr 0.089
r_metal_ion_refined 0.009
r_mcangle_it 2.602
r_symmetry_vdw_other 0.312
r_mcbond_it 1.515
r_symmetry_vdw_refined 0.236
r_nbd_other 0.239
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5842
Nucleic Acid Atoms 0
Heterogen Atoms 36
Solvent Atoms 132

Software

Software
Software Name Purpose
PHASER phasing
REFMAC refinement version: 5.2.0005
XDS data reduction
XSCALE data scaling