X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details BuamA.10647.a.B2.PS37954 at 23.88 mg/mL against MCSG1 screen condition E5 0.1 M MES pH 6.5, 1.6 M MgSO4, crystal tracking ID 282706e5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.8 α = 90
b = 74.31 β = 90
c = 137.17 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944+ -- 2017-02-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418 -- --

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
1.65 40.66 99.9 0.059 -- -- 7.396 -- 42618 -- -3.0 20.72
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)
1.65 1.69 99.7 0.461 -- 3.92 7.427 --

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
SAD 1.65 40.658 -- 1.35 -- 42613 2049 99.89 -- 0.1602 0.1588 0.1866 --
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 1.65 1.6883 -- 130 2714 0.2199 0.2323 0.0 100.0
X Ray Diffraction 1.6883 1.7306 -- 132 2617 0.1935 0.2416 0.0 100.0
X Ray Diffraction 1.7306 1.7774 -- 141 2665 0.1812 0.2121 0.0 100.0
X Ray Diffraction 1.7774 1.8297 -- 130 2691 0.1715 0.2167 0.0 100.0
X Ray Diffraction 1.8297 1.8887 -- 136 2688 0.1624 0.1915 0.0 100.0
X Ray Diffraction 1.8887 1.9562 -- 140 2677 0.1624 0.1817 0.0 100.0
X Ray Diffraction 1.9562 2.0345 -- 136 2676 0.1668 0.2056 0.0 100.0
X Ray Diffraction 2.0345 2.1271 -- 135 2684 0.1568 0.1996 0.0 100.0
X Ray Diffraction 2.1271 2.2393 -- 132 2697 0.1531 0.1699 0.0 100.0
X Ray Diffraction 2.2393 2.3796 -- 106 2733 0.1563 0.1935 0.0 100.0
X Ray Diffraction 2.3796 2.5633 -- 147 2702 0.1603 0.1713 0.0 100.0
X Ray Diffraction 2.5633 2.8211 -- 159 2698 0.1632 0.1901 0.0 100.0
X Ray Diffraction 2.8211 3.2292 -- 115 2734 0.1642 0.1668 0.0 100.0
X Ray Diffraction 3.2292 4.0679 -- 130 2768 0.1433 0.1771 0.0 100.0
X Ray Diffraction 4.0679 40.6699 -- 180 2820 0.1537 0.1891 0.0 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.8883
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 9.583
f_chiral_restr 0.052
f_plane_restr 0.006
f_bond_d 0.005
f_angle_d 0.773
Coordinate Error
Parameter Value
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2305
Nucleic Acid Atoms 0
Heterogen Atoms 25
Solvent Atoms 299

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing
PHENIX refinement
PDB_EXTRACT data extraction version: 3.22
XDS data reduction