X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.8
Temperature 293.0
Details 50 mM tris-HCl, 1.2 M sodium citrate, 5 + 5 uL droplet, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.36 α = 90
b = 41.45 β = 104.24
c = 71.96 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2009-04-30
Diffraction Radiation
Monochromator Protocol
Rigaku varimax SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 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
1.5 20 92.3 0.076 0.076 -- 7.1 36024 36024 0.0 0.0 --
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 87.4 -- -- 5.1 6.9 --

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 1.5 19.968 -- 0.0 36024 35511 1762 91.04 -- 0.1419 0.1404 0.1712 --
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 1.5406 -- 126 2350 0.3127 0.3694 -- 84.0
X Ray Diffraction 1.5406 1.5859 -- 128 2406 0.228 0.2708 -- 85.0
X Ray Diffraction 1.5859 1.6371 -- 118 2455 0.1663 0.2146 -- 86.0
X Ray Diffraction 1.6371 1.6955 -- 140 2487 0.1465 0.1827 -- 88.0
X Ray Diffraction 1.6955 1.7634 -- 126 2511 0.1277 0.1671 -- 89.0
X Ray Diffraction 1.7634 1.8436 -- 138 2555 0.1253 0.1781 -- 90.0
X Ray Diffraction 1.8436 1.9407 -- 133 2579 0.1236 0.1584 -- 91.0
X Ray Diffraction 1.9407 2.0622 -- 130 2642 0.1306 0.1615 -- 92.0
X Ray Diffraction 2.0622 2.2212 -- 145 2630 0.1315 0.162 -- 93.0
X Ray Diffraction 2.2212 2.4444 -- 138 2716 0.1312 0.1588 -- 95.0
X Ray Diffraction 2.4444 2.7973 -- 139 2725 0.1347 0.1777 -- 95.0
X Ray Diffraction 2.7973 3.5211 -- 150 2799 0.1324 0.1692 -- 97.0
X Ray Diffraction 3.5211 19.9697 -- 151 2894 0.1399 0.1488 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.3595
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.326
Anisotropic B[2][2] -0.414
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.7735
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.513
f_plane_restr 0.009
f_bond_d 0.012
f_dihedral_angle_d 13.747
f_chiral_restr 0.083
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2059
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 306

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.7_650
PDB_EXTRACT data extraction version: 3.100
CrystalClear data collection
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing