X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 295.0
Details 20% PEG5000 MME, 50 mM MES pH 6.5, 2mM CaCl2, 250mM NaCl, 5% glycerol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.58 α = 90
b = 73.56 β = 90
c = 83.28 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 -- 2015-09-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-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 50 98.0 0.053 -- -- 5.7 -- 68848 -- -- 17.5
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 91.0 0.864 -- 1.64 4.7 --

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
-- 1.5 43.448 -- 1.35 -- 68829 3442 98.29 -- 0.15 0.1489 0.1707 0
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 1.5206 -- 118 2248 0.3045 0.2709 -- 86.0
X Ray Diffraction 1.5206 1.5423 -- 128 2416 0.2804 0.2871 -- 91.0
X Ray Diffraction 1.5423 1.5653 -- 136 2594 0.2553 0.3038 -- 99.0
X Ray Diffraction 1.5653 1.5898 -- 137 2599 0.2373 0.2559 -- 100.0
X Ray Diffraction 1.5898 1.6158 -- 138 2623 0.2181 0.2442 -- 100.0
X Ray Diffraction 1.6158 1.6437 -- 141 2660 0.2068 0.2193 -- 100.0
X Ray Diffraction 1.6437 1.6736 -- 137 2617 0.1968 0.1841 -- 100.0
X Ray Diffraction 1.6736 1.7058 -- 139 2641 0.1886 0.1986 -- 100.0
X Ray Diffraction 1.7058 1.7406 -- 138 2614 0.1724 0.1854 -- 100.0
X Ray Diffraction 1.7406 1.7784 -- 138 2641 0.1684 0.209 -- 100.0
X Ray Diffraction 1.7784 1.8198 -- 139 2644 0.1588 0.1702 -- 100.0
X Ray Diffraction 1.8198 1.8653 -- 138 2619 0.1515 0.1836 -- 100.0
X Ray Diffraction 1.8653 1.9158 -- 140 2649 0.1414 0.1647 -- 100.0
X Ray Diffraction 1.9158 1.9721 -- 138 2628 0.1407 0.1888 -- 100.0
X Ray Diffraction 1.9721 2.0358 -- 139 2648 0.1376 0.1625 -- 100.0
X Ray Diffraction 2.0358 2.1085 -- 138 2618 0.1366 0.1352 -- 100.0
X Ray Diffraction 2.1085 2.193 -- 141 2679 0.1318 0.1565 -- 100.0
X Ray Diffraction 2.193 2.2928 -- 137 2606 0.1317 0.1658 -- 99.0
X Ray Diffraction 2.2928 2.4136 -- 140 2658 0.1275 0.144 -- 99.0
X Ray Diffraction 2.4136 2.5648 -- 139 2642 0.1337 0.1516 -- 99.0
X Ray Diffraction 2.5648 2.7628 -- 140 2643 0.139 0.1734 -- 99.0
X Ray Diffraction 2.7628 3.0408 -- 139 2652 0.1397 0.1822 -- 98.0
X Ray Diffraction 3.0408 3.4807 -- 139 2646 0.1363 0.1413 -- 97.0
X Ray Diffraction 3.4807 4.3846 -- 140 2660 0.1237 0.1537 -- 97.0
X Ray Diffraction 4.3846 43.4664 -- 145 2742 0.1568 0.1702 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.5202
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.01
f_bond_d 0.013
f_chiral_restr 0.072
f_angle_d 1.299
f_dihedral_angle_d 14.893
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3249
Nucleic Acid Atoms 0
Heterogen Atoms 89
Solvent Atoms 351

Software

Software
Software Name Purpose
PHENIX refinement version: 1.10.1_2155
PDB_EXTRACT data extraction version: 3.20
XDS data reduction
XSCALE data scaling
PHASER phasing