X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.9
Temperature 277.0
Details NANODROP, 0.2M Potassium nitrate, 20.0% PEG 3350, No Buffer pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Method Vapor Diffusion Sitting Drop
Temperature 277.0
Details NANODROP, 0.2M Potassium nitrate, 20.0% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 113.51 α = 90
b = 113.51 β = 90
c = 55.94 γ = 120
Symmetry
Space Group P 64

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 collimating mirror, toroid focusing mirror 2006-06-18
CCD ADSC QUANTUM 315 -- 2006-09-22
Diffraction Radiation
Monochromator Protocol
Single, cylindrically bent, asymmetrically cut Si(220) crystal SINGLE WAVELENGTH
Double crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.3 1.00000 ALS 5.0.3
SYNCHROTRON SSRL BEAMLINE BL9-2 0.97922, 0.97939, 0.91162 SSRL BL9-2

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
2.3 28.27 97.3 0.052 -- -- 3.66 -- 18260 -- -- 46.09
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)
2.3 2.38 92.9 0.41 -- 1.76 -- --

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 2.3 28.273 -- 0.0 -- 18113 922 98.39 0.175 0.175 0.173 0.225 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 2.3 2.362 1300 57 1243 0.252 0.307 -- 97.6
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 60.7
Anisotropic B[1][1] 0.08
Anisotropic B[1][2] 0.04
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.08
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.12
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.002
r_angle_refined_deg 1.449
r_gen_planes_refined 0.005
r_mcbond_it 1.742
r_chiral_restr 0.076
r_nbtor_other 0.088
r_symmetry_vdw_other 0.254
r_symmetry_hbond_refined 0.11
r_dihedral_angle_4_deg 18.875
r_dihedral_angle_1_deg 7.053
r_nbd_refined 0.217
r_xyhbond_nbd_refined 0.134
r_mcbond_other 0.362
r_bond_refined_d 0.013
r_scbond_it 5.366
r_dihedral_angle_3_deg 13.499
r_gen_planes_other 0.001
r_angle_other_deg 0.926
r_scangle_it 6.955
r_dihedral_angle_2_deg 33.576
r_nbd_other 0.204
r_mcangle_it 2.897
r_nbtor_refined 0.174
r_symmetry_vdw_refined 0.167
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1846
Nucleic Acid Atoms 0
Heterogen Atoms 64
Solvent Atoms 113

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
SOLVE phasing
REFMAC refinement version: 5.2.0019
XSCALE data scaling
PDB_EXTRACT data extraction version: 2.000
ADSC data collection version: QUANTUM
XDS data reduction