X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 10% PEG 8000, 5% iso-propanol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.61 α = 90
b = 68.29 β = 91.47
c = 93.96 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR scanner 300 mm plate -- 2011-06-23
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1 APS 22-BM

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
2.4 50 83.6 0.059 0.076 -- 3.5 32234 26948 0.0 0.0 41.97
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)
2.4 2.44 27.9 0.401 0.48 1.7 2.2 --

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 2.4 28.461 -- 1.37 32160 26844 1307 83.47 -- 0.2035 0.2004 0.2626 --
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 2.4004 2.4964 -- 49 1081 0.272 0.3506 -- 32.0
X Ray Diffraction 2.4964 2.61 -- 94 1775 0.2687 0.3496 -- 52.0
X Ray Diffraction 2.61 2.7474 -- 137 2546 0.2667 0.3086 -- 75.0
X Ray Diffraction 2.7474 2.9194 -- 173 3162 0.2615 0.3489 -- 95.0
X Ray Diffraction 2.9194 3.1446 -- 151 3362 0.2442 0.348 -- 98.0
X Ray Diffraction 3.1446 3.4605 -- 183 3332 0.2208 0.2765 -- 99.0
X Ray Diffraction 3.4605 3.9601 -- 168 3399 0.1859 0.2618 -- 99.0
X Ray Diffraction 3.9601 4.985 -- 161 3422 0.167 0.2138 -- 100.0
X Ray Diffraction 4.985 28.463 -- 191 3458 0.1798 0.2321 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 64.1823
Anisotropic B[1][1] 7.2426
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -5.736
Anisotropic B[2][2] 0.3146
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.5573
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.001
f_chiral_restr 0.025
f_dihedral_angle_d 10.848
f_angle_d 0.403
f_bond_d 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5308
Nucleic Acid Atoms 0
Heterogen Atoms 384
Solvent Atoms 96

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASES Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement