X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 3.7
Temperature 277.0
Details 0.1 M Na tri-citrate pH 3.7, 2.6 M Na formate, 0.5% (w/v) polyvinylpyrrolidone K15

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.95 α = 90
b = 54.95 β = 90
c = 117.43 γ = 90
Symmetry
Space Group P 43

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2013-02-25
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I911-3 0.9792 MAX II I911-3

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
1.4 50 99.8 0.064 -- -- 4.2 -- 68172 2.0 -3.0 12.02
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)
1.4 1.5 99.8 0.742 -- 2.33 4.1 --

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 1.4 36.889 -- 2.0 -- 68165 3452 99.8 -- 0.1457 0.1442 0.174 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 1.4 1.4192 -- 143 2595 0.2392 0.2879 -- 100.0
X Ray Diffraction 1.4192 1.4395 -- 156 2605 0.223 0.2541 -- 100.0
X Ray Diffraction 1.4395 1.461 -- 126 2549 0.1952 0.2787 -- 100.0
X Ray Diffraction 1.461 1.4838 -- 142 2606 0.1839 0.2111 -- 100.0
X Ray Diffraction 1.4838 1.5081 -- 148 2545 0.1611 0.2195 -- 100.0
X Ray Diffraction 1.5081 1.5341 -- 131 2607 0.1502 0.1931 -- 100.0
X Ray Diffraction 1.5341 1.562 -- 152 2571 0.1364 0.1769 -- 100.0
X Ray Diffraction 1.562 1.5921 -- 128 2594 0.1272 0.1764 -- 100.0
X Ray Diffraction 1.5921 1.6246 -- 127 2598 0.129 0.1415 -- 100.0
X Ray Diffraction 1.6246 1.6599 -- 164 2585 0.1198 0.1697 -- 100.0
X Ray Diffraction 1.6599 1.6985 -- 134 2559 0.1147 0.1374 -- 100.0
X Ray Diffraction 1.6985 1.741 -- 128 2575 0.1153 0.1492 -- 100.0
X Ray Diffraction 1.741 1.7881 -- 142 2589 0.1186 0.1769 -- 100.0
X Ray Diffraction 1.7881 1.8407 -- 145 2579 0.1285 0.1741 -- 100.0
X Ray Diffraction 1.8407 1.9001 -- 139 2587 0.1281 0.1433 -- 100.0
X Ray Diffraction 1.9001 1.968 -- 140 2584 0.1265 0.1504 -- 100.0
X Ray Diffraction 1.968 2.0468 -- 114 2623 0.1254 0.1502 -- 100.0
X Ray Diffraction 2.0468 2.1399 -- 131 2575 0.125 0.1612 -- 100.0
X Ray Diffraction 2.1399 2.2527 -- 137 2572 0.1222 0.1548 -- 100.0
X Ray Diffraction 2.2527 2.3938 -- 129 2645 0.1229 0.161 -- 100.0
X Ray Diffraction 2.3938 2.5786 -- 128 2570 0.136 0.171 -- 100.0
X Ray Diffraction 2.5786 2.838 -- 150 2608 0.1518 0.1819 -- 100.0
X Ray Diffraction 2.838 3.2485 -- 138 2604 0.1662 0.1991 -- 100.0
X Ray Diffraction 3.2485 4.0919 -- 145 2580 0.1445 0.1572 -- 100.0
X Ray Diffraction 4.0919 36.9014 -- 135 2608 0.1679 0.1807 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.19
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.008
f_chiral_restr 0.065
f_dihedral_angle_d 13.726
f_angle_d 1.198
f_plane_restr 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms --
Nucleic Acid Atoms --
Heterogen Atoms 48
Solvent Atoms 333

Software

Software
Software Name Purpose
XDS data scaling
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.14
PHASER phasing
PHENIX refinement version: (phenix.refine: dev_1593)