X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 298.0
Details 25% PEG3350, 100mM Na Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.06 α = 90
b = 65.85 β = 90
c = 89.04 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD bimorph KB mirrors 2011-07-09
Diffraction Radiation
Monochromator Protocol
Si(111) double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 0.88567 APS 21-ID-D

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
0.95 30 99.3 0.053 -- -- 5.8 140927 139941 1.5 2.2 11.15
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)
0.95 0.98 93.5 0.486 -- 2.2 3.5 13024

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 0.95 30.0 -- 1.34 141350 139838 6995 98.9 0.1373 0.1371 0.1363 0.1524 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 0.95 0.9839 12585 630 3376 0.2737 0.2795 -- 90.1
X Ray Diffraction 0.9839 1.0233 13887 694 4196 0.1831 0.1993 -- 99.4
X Ray Diffraction 1.0233 1.0699 13992 701 4383 0.1355 0.1558 -- 99.9
X Ray Diffraction 1.0699 1.1263 14040 702 4400 0.1106 0.1277 -- 100.0
X Ray Diffraction 1.1263 1.1969 14048 702 4406 0.104 0.1221 -- 100.0
X Ray Diffraction 1.1969 1.2893 14064 704 4388 0.1077 0.1227 -- 100.0
X Ray Diffraction 1.2893 1.419 14113 705 4450 0.1093 0.134 -- 100.0
X Ray Diffraction 1.419 1.6244 14165 709 4399 0.1118 0.1337 -- 100.0
X Ray Diffraction 1.6244 2.0465 14238 712 4441 0.1334 0.1504 -- 99.8
X Ray Diffraction 2.0465 28.9451 14703 236 4480 0.1503 0.1624 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.3
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.096
f_plane_restr 0.008
f_angle_d 1.577
f_bond_d 0.01
f_dihedral_angle_d 13.167
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1851
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 345

Software

Software
Software Name Purpose
PHENIX refinement version: 1.7.3_928
PDB_EXTRACT data extraction version: 3.10
BLU-MAX data collection
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing