X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 285.0
Details 16 20% (w/v) PEG 3350, 0.2 M NH4-acetate, 0.1 M Bis-TRIS pH 6.1 6.7, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 285K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.66 α = 90
b = 64.66 β = 90
c = 160.95 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD Si(111)monochromator 2006-02-22
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 0.9786 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
1.9 20 99.5 0.059 -- -- 8.3 31581 31421 -- 3.0 37.0
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)
1.9 2.0 99.4 0.374 -- 3.9 7.6 4408

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
-- 1.9 19.69 -- 0.0 -- 31420 1582 99.62 -- 0.188 0.186 0.245 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 -- 125 2130 0.263 0.35 -- 99.38
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.187
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 1.041
r_nbtor_other 0.085
r_symmetry_vdw_other 0.276
r_bond_other_d 0.001
r_nbtor_refined 0.18
r_scbond_it 4.368
r_scangle_it 6.014
r_dihedral_angle_4_deg 18.634
r_dihedral_angle_2_deg 34.697
r_dihedral_angle_1_deg 6.709
r_nbd_other 0.215
r_symmetry_hbond_refined 0.244
r_gen_planes_refined 0.007
r_gen_planes_other 0.002
r_xyhbond_nbd_refined 0.208
r_mcangle_it 3.121
r_mcbond_it 2.467
r_mcbond_other 3.065
r_nbd_refined 0.206
r_angle_refined_deg 1.686
r_symmetry_vdw_refined 0.201
r_chiral_restr 0.223
r_dihedral_angle_3_deg 16.025
r_bond_refined_d 0.02
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2701
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 156

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.000
XDS data scaling
XDS data reduction
XSCALE data scaling
SHELXD phasing