X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 277.0
Details NANODROP, 8.0% PEG 4000, 0.1M Acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 277.0
Details NANODROP, 0.2M Li2SO4, 40.0% PEG 400, 0.1M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.07 α = 90
b = 79.07 β = 90
c = 181.26 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-01-18
CCD MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-01-07
Diffraction Radiation
Monochromator Protocol
Single crystal Si(111) bent (horizontal focusing) MAD
Single crystal Si(111) bent (horizontal focusing) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.97917, 0.91837, 0.97886 SSRL BL11-1
SYNCHROTRON SSRL BEAMLINE BL11-1 0.91162 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 27.64 99.5 0.071 -- -- 17.62 -- 27197 -- -- 32.59
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 99.3 0.905 -- 2.0 -- --

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
MAD, MOLECULAR REPLACEMENT 1.9 27.64 -- 0.0 -- 27120 1363 99.48 0.195 0.195 0.193 0.242 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 1.9 1.949 1930 87 1843 0.285 0.377 -- 99.13
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.353
Anisotropic B[1][1] 1.77
Anisotropic B[1][2] 0.89
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.77
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.66
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.529
r_gen_planes_other 0.001
r_dihedral_angle_2_deg 37.366
r_chiral_restr 0.149
r_bond_other_d 0.001
r_scbond_it 5.4
r_scangle_it 7.142
r_dihedral_angle_3_deg 12.391
r_gen_planes_refined 0.006
r_nbtor_refined 0.181
r_nbtor_other 0.086
r_symmetry_vdw_refined 0.037
r_symmetry_vdw_other 0.195
r_mcbond_it 2.37
r_angle_refined_deg 1.609
r_nbd_other 0.187
r_xyhbond_nbd_refined 0.205
r_mcangle_it 3.613
r_nbd_refined 0.225
r_bond_refined_d 0.016
r_dihedral_angle_4_deg 15.97
r_angle_other_deg 1.095
r_mcbond_other 0.603
r_symmetry_hbond_refined 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1375
Nucleic Acid Atoms 0
Heterogen Atoms 36
Solvent Atoms 151

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
REFMAC refinement version: 5.2.0005
XSCALE data scaling
PDB_EXTRACT data extraction version: 2.000
Blu-Ice data collection version: v 5.0
XDS data reduction
MOSFLM data reduction
SCALA data scaling
SHELXD phasing
autoSHARP phasing
PHASER phasing