X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.2
Temperature 298.0
Details 1.5 M ammonium sulphate, 0.17 M Guanidine HCl, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 26.11 α = 90
b = 54.16 β = 90
c = 101.63 γ = 90
Symmetry
Space Group P 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2010-11-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID -- APS 22-ID

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
1.5 50 96.8 0.109 -- -- 4.8 -- n/a -- -- --
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)
1.5 1.55 90.7 0.538 -- -- 4.3 --

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
SIRAS 1.5 27.08 -- 1.35 -- 23029 1178 95.9 -- 0.141 0.139 0.182 --
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 1.5 1.5668 -- 115 2247 0.2011 0.2825 -- 80.0
X Ray Diffraction 1.5668 1.6494 -- 143 2598 0.1836 0.2182 -- 93.0
X Ray Diffraction 1.6494 1.7528 -- 171 2740 0.1522 0.2065 -- 98.0
X Ray Diffraction 1.7528 1.8881 -- 147 2754 0.1259 0.2002 -- 98.0
X Ray Diffraction 1.8881 2.078 -- 144 2793 0.1091 0.1509 -- 99.0
X Ray Diffraction 2.078 2.3786 -- 149 2814 0.1156 0.1507 -- 99.0
X Ray Diffraction 2.3786 2.9961 -- 145 2878 0.1325 0.1686 -- 99.0
X Ray Diffraction 2.9961 27.0864 -- 164 3027 0.149 0.1836 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.07
Anisotropic B[1][1] -1.6641
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.5375
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.8734
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.317
f_dihedral_angle_d 13.775
f_angle_d 1.393
f_bond_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1073
Nucleic Acid Atoms 0
Heterogen Atoms 76
Solvent Atoms 146

Software

Computing
Computing Package Purpose
HKL Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
SOLVE Structure Solution
PHENIX (PHENIX.REFINE: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
DM density modification
SOLVE phasing
SCALEPACK data reduction