X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 293.15
Details PEG 1500 25 % Sodium chloride 0.2 M Sodium cacodylate 0.1 M

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.77 α = 90
b = 90.59 β = 114.14
c = 53.42 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 2M -- 2017-09-29
Diffraction Radiation
Monochromator Protocol
C(110) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-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
1.5 48.75 96.3 0.036 -- -- 3.1 -- 65618 -- -- 18.631
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)
1.496 1.522 95.1 0.526 -- 2.1 2.8 --

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 1.49608 48.748 -- 1.35027 -- 65613 3073 96.2321 -- 0.17069 0.169058 0.203371 --
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 1.4961 1.5195 -- 117 2795 0.221672 0.273801 -- 94.6376
X Ray Diffraction 1.5195 1.5444 -- 157 2778 0.226223 0.291297 -- 95.2922
X Ray Diffraction 1.5444 1.571 -- 125 2825 0.227232 0.254421 -- 94.7335
X Ray Diffraction 1.571 1.5996 -- 137 2804 0.221787 0.265839 -- 95.7045
X Ray Diffraction 1.5996 1.6303 -- 138 2837 0.21298 0.278366 -- 95.6284
X Ray Diffraction 1.6303 1.6636 -- 142 2801 0.21152 0.264829 -- 96.0196
X Ray Diffraction 1.6636 1.6998 -- 144 2801 0.211201 0.248903 -- 95.8347
X Ray Diffraction 1.6998 1.7393 -- 141 2854 0.195619 0.232837 -- 95.9628
X Ray Diffraction 1.7393 1.7828 -- 158 2831 0.176543 0.223692 -- 96.7001
X Ray Diffraction 1.7828 1.831 -- 141 2825 0.16663 0.252852 -- 96.8964
X Ray Diffraction 1.831 1.8849 -- 158 2846 0.15695 0.18781 -- 97.0911
X Ray Diffraction 1.8849 1.9458 -- 164 2870 0.146259 0.204473 -- 97.5563
X Ray Diffraction 1.9458 2.0153 -- 167 2832 0.141572 0.203656 -- 96.9609
X Ray Diffraction 2.0153 2.096 -- 101 2858 0.141058 0.160133 -- 96.1026
X Ray Diffraction 2.096 2.1914 -- 131 2888 0.143824 0.177408 -- 96.887
X Ray Diffraction 2.1914 2.3069 -- 131 2902 0.145015 0.179811 -- 97.5869
X Ray Diffraction 2.3069 2.4515 -- 98 2942 0.157585 0.191875 -- 97.561
X Ray Diffraction 2.4515 2.6407 -- 117 2885 0.177976 0.222005 -- 97.5943
X Ray Diffraction 2.6407 2.9064 -- 148 2871 0.17708 0.203941 -- 97.0428
X Ray Diffraction 2.9064 3.3269 -- 162 2842 0.177601 0.196674 -- 96.2821
X Ray Diffraction 3.3269 4.1912 -- 159 2774 0.161228 0.174937 -- 94.491
X Ray Diffraction 4.1912 48.7739 -- 137 2879 0.171654 0.209418 -- 94.6642
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.6128
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 4.32312
f_chiral_restr 0.0869537
f_bond_d 0.00684656
f_angle_d 0.905514
f_plane_restr 0.00594429
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3354
Nucleic Acid Atoms 0
Heterogen Atoms 96
Solvent Atoms 227

Software

Software
Software Name Purpose
AutoPROC data processing version: 1.1.7
PHASER phasing version: 2.8.0
Coot model building version: 0.8.2
PHENIX refinement version: 1.12_2829
XDS data reduction
XSCALE data scaling