X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9
Temperature 295.0
Details 0.1M Tris/HCl pH 9.0, 25% P400, 0.2M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 152.8 α = 90
b = 165.11 β = 90
c = 180.58 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
PIXEL DECTRIS PILATUS 6M -- 2011-08-31
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 1 SLS X10SA

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
3.3 49.02 99.8 0.1721 0.1721 -- 7.3 -- 69239 -- -- --
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)
3.3 3.4 100.0 0.8579 0.8579 1.06 7.8 --

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 3.3 49.02 -- 1.33 -- 68987 3489 99.56 -- 0.177 0.174 0.2349 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 3.3 3.3452 -- 131 2586 0.3518 0.4033 -- 100.0
X Ray Diffraction 3.3452 3.393 -- 129 2604 0.3457 0.3735 -- 100.0
X Ray Diffraction 3.393 3.4436 -- 166 2528 0.3486 0.441 -- 99.0
X Ray Diffraction 3.4436 3.4974 -- 126 2546 0.3402 0.3856 -- 99.0
X Ray Diffraction 3.4974 3.5547 -- 136 2614 0.3037 0.3801 -- 99.0
X Ray Diffraction 3.5547 3.616 -- 139 2580 0.3069 0.3433 -- 100.0
X Ray Diffraction 3.616 3.6818 -- 142 2567 0.2977 0.3455 -- 99.0
X Ray Diffraction 3.6818 3.7525 -- 143 2602 0.2681 0.3519 -- 99.0
X Ray Diffraction 3.7525 3.8291 -- 126 2621 0.2641 0.3389 -- 100.0
X Ray Diffraction 3.8291 3.9123 -- 142 2557 0.2562 0.3444 -- 99.0
X Ray Diffraction 3.9123 4.0033 -- 155 2602 0.2332 0.2956 -- 100.0
X Ray Diffraction 4.0033 4.1034 -- 122 2609 0.2146 0.2868 -- 100.0
X Ray Diffraction 4.1034 4.2143 -- 131 2620 0.1969 0.2827 -- 100.0
X Ray Diffraction 4.2143 4.3382 -- 142 2605 0.1813 0.2487 -- 100.0
X Ray Diffraction 4.3382 4.4781 -- 161 2600 0.1769 0.2554 -- 100.0
X Ray Diffraction 4.4781 4.6381 -- 157 2591 0.1581 0.2197 -- 100.0
X Ray Diffraction 4.6381 4.8236 -- 140 2617 0.1435 0.2086 -- 100.0
X Ray Diffraction 4.8236 5.0429 -- 131 2625 0.1405 0.2487 -- 100.0
X Ray Diffraction 5.0429 5.3085 -- 159 2630 0.1444 0.2121 -- 100.0
X Ray Diffraction 5.3085 5.6407 -- 131 2658 0.1485 0.239 -- 100.0
X Ray Diffraction 5.6407 6.0754 -- 145 2642 0.1535 0.2158 -- 100.0
X Ray Diffraction 6.0754 6.6855 -- 124 2671 0.1608 0.25 -- 100.0
X Ray Diffraction 6.6855 7.6497 -- 125 2706 0.1657 0.2422 -- 100.0
X Ray Diffraction 7.6497 9.6259 -- 132 2717 0.1194 0.1788 -- 100.0
X Ray Diffraction 9.6259 49.027 -- 154 2800 0.1392 0.1479 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 3.8982
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -16.1532
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 12.255
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.083
f_dihedral_angle_d 17.804
f_angle_d 1.296
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 21647
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 3

Software

Computing
Computing Package Purpose
beamline software Data Collection
XDS (VERSION December 6, 2010) Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: dev_934) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: dev_934) refinement
PHASER model building
beamline version: software data collection