X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 277.0
Details 100MM HEPES, 200MM MGCL2, 33% PEG 400, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 107.94 α = 90
b = 107.94 β = 90
c = 174.95 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 180
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ -- 2012-01-05
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 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
2.5 53.97 99.3 0.11 0.11 -- 4.22 -- 41167 0.0 0.0 40.8
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)
2.5 2.59 98.7 0.376 0.376 2.2 4.27 --

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 2.5 49.477 -- 1.37 -- 41052 2070 99.02 -- 0.2184 0.217 0.244 --
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 2.5001 2.5583 -- 135 2529 0.2734 0.3181 -- 98.0
X Ray Diffraction 2.5583 2.6222 -- 146 2537 0.2584 0.3067 -- 98.0
X Ray Diffraction 2.6222 2.6931 -- 120 2584 0.2781 0.2925 -- 98.0
X Ray Diffraction 2.6931 2.7724 -- 139 2545 0.2672 0.3112 -- 99.0
X Ray Diffraction 2.7724 2.8618 -- 123 2579 0.2345 0.2841 -- 99.0
X Ray Diffraction 2.8618 2.9641 -- 151 2545 0.2328 0.2471 -- 99.0
X Ray Diffraction 2.9641 3.0828 -- 154 2544 0.2501 0.2771 -- 99.0
X Ray Diffraction 3.0828 3.223 -- 138 2580 0.2424 0.2651 -- 99.0
X Ray Diffraction 3.223 3.3929 -- 132 2588 0.2468 0.304 -- 99.0
X Ray Diffraction 3.3929 3.6055 -- 148 2617 0.2308 0.2237 -- 99.0
X Ray Diffraction 3.6055 3.8837 -- 139 2602 0.2354 0.2746 -- 100.0
X Ray Diffraction 3.8837 4.2744 -- 152 2612 0.1992 0.229 -- 100.0
X Ray Diffraction 4.2744 4.8924 -- 138 2657 0.1748 0.2184 -- 100.0
X Ray Diffraction 4.8924 6.1621 -- 131 2663 0.1931 0.2132 -- 100.0
X Ray Diffraction 6.1621 49.4869 -- 124 2800 0.1994 0.1967 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 73.277
Anisotropic B[1][1] 3.35
Anisotropic B[1][2] 1.67
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.35
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.02
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.09
f_dihedral_angle_d 15.696
f_angle_d 1.137
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4611
Nucleic Acid Atoms 0
Heterogen Atoms 85
Solvent Atoms 254

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0109 refinement
PHASER model building
HKL-2000 data collection