X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Batch Mode
pH 6.1
Temperature 277.0
Details PEG1450, glycerol, MES-NaOH, CaCl2, beta-DDM

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 210.45 α = 90
b = 240.31 β = 90
c = 300.06 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 MX225HE -- 2011-01-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.9 SPRING-8 BL41XU

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
2.77 29.77 99.4 0.104 -- -- 7.5 -- 382176 -- -- 67.7884
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)
2.76 2.93 97.7 1.162 -- 2.04 7.15 --

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
-- 2.77 9.99957 -- 1.33646 -- 373681 18739 99.7464 -- 0.250629 0.249196 0.277701 --
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 2.77 2.8008 -- 596 11225 0.377425 0.402552 -- 95.2462
X Ray Diffraction 2.8008 2.833 -- 620 11763 0.340308 0.394879 -- 99.8951
X Ray Diffraction 2.833 2.8668 -- 637 11785 0.334244 0.380536 -- 99.9356
X Ray Diffraction 2.8668 2.9022 -- 633 11762 0.326554 0.374371 -- 99.9033
X Ray Diffraction 2.9022 2.9394 -- 565 11823 0.332653 0.390294 -- 99.9355
X Ray Diffraction 2.9394 2.9786 -- 618 11815 0.318016 0.365605 -- 99.9678
X Ray Diffraction 2.9786 3.02 -- 616 11769 0.310297 0.357502 -- 99.9193
X Ray Diffraction 3.02 3.0638 -- 688 11739 0.307787 0.36319 -- 99.9357
X Ray Diffraction 3.0638 3.1103 -- 643 11768 0.295347 0.343429 -- 99.9436
X Ray Diffraction 3.1103 3.1597 -- 648 11794 0.299112 0.339794 -- 99.9438
X Ray Diffraction 3.1597 3.2124 -- 604 11806 0.281798 0.324314 -- 99.9195
X Ray Diffraction 3.2124 3.2688 -- 591 11826 0.277667 0.320834 -- 99.9597
X Ray Diffraction 3.2688 3.3294 -- 615 11839 0.274852 0.314141 -- 99.9118
X Ray Diffraction 3.3294 3.3948 -- 597 11873 0.258674 0.297261 -- 99.9199
X Ray Diffraction 3.3948 3.4656 -- 647 11727 0.26266 0.308521 -- 99.9435
X Ray Diffraction 3.4656 3.5427 -- 609 11855 0.263353 0.301402 -- 99.9759
X Ray Diffraction 3.5427 3.6272 -- 622 11856 0.256646 0.295473 -- 99.9119
X Ray Diffraction 3.6272 3.7203 -- 618 11813 0.255479 0.309748 -- 99.9437
X Ray Diffraction 3.7203 3.8239 -- 628 11853 0.248243 0.286835 -- 99.856
X Ray Diffraction 3.8239 3.94 -- 597 11869 0.242022 0.266538 -- 99.8158
X Ray Diffraction 3.94 4.0716 -- 618 11860 0.237043 0.272519 -- 99.824
X Ray Diffraction 4.0716 4.2228 -- 619 11871 0.23707 0.264263 -- 99.7604
X Ray Diffraction 4.2228 4.3993 -- 683 11766 0.229052 0.247163 -- 99.7676
X Ray Diffraction 4.3993 4.6095 -- 601 11897 0.222199 0.249799 -- 99.7207
X Ray Diffraction 4.6095 4.8668 -- 621 11900 0.219978 0.235699 -- 99.7928
X Ray Diffraction 4.8668 5.1932 -- 640 11904 0.227163 0.253587 -- 99.8885
X Ray Diffraction 5.1932 5.6295 -- 656 11936 0.2385 0.254348 -- 99.9206
X Ray Diffraction 5.6295 6.2632 -- 623 12024 0.244663 0.253246 -- 99.9763
X Ray Diffraction 6.2632 7.3339 -- 609 12077 0.23024 0.262299 -- 99.9764
X Ray Diffraction 7.3339 9.9996 -- 677 12147 0.205826 0.211219 -- 99.961
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 68.5704
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.4296
f_plane_restr 0.00495866
f_chiral_restr 0.0392767
f_angle_d 1.18202
f_bond_d 0.00614951
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 77709
Nucleic Acid Atoms 0
Heterogen Atoms 15016
Solvent Atoms 18

Software

Computing
Computing Package Purpose
PHENIX (phenix.refine: 1.9_1692) Structure Refinement
Software
Software Name Purpose
SOLVE phasing
SHARP phasing
XDS data scaling
XDS data reduction
PHENIX version: 1.9_1692 refinement