X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 289.0
Details 2.9M sodium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 107.6 α = 90
b = 122.51 β = 90
c = 405.53 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2011-12-17
CCD ADSC QUANTUM 210 -- 2011-07-11
Diffraction Radiation
Monochromator Protocol
-- MAD
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.97865, 0.97935 PHOTON FACTORY BL-17A
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 PHOTON FACTORY BL-5A

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
2.7 50 99.1 0.073 -- -- 5.7 -- 146526 -- -- --
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)
2.7 2.8 100.0 0.522 -- -- 5.7 14598

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
MAD 2.757 37.548 -- 1.34 -- 136168 2468 98.07 -- 0.2366 0.2362 0.257 --
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 2.7575 2.8105 -- 126 6807 0.3383 0.3085 -- 91.0
X Ray Diffraction 2.8105 2.8679 -- 153 7434 0.3484 0.3902 -- 100.0
X Ray Diffraction 2.8679 2.9302 -- 127 7471 0.3392 0.3588 -- 100.0
X Ray Diffraction 2.9302 2.9983 -- 147 7501 0.3248 0.3495 -- 100.0
X Ray Diffraction 2.9983 3.0733 -- 138 7491 0.3154 0.3358 -- 100.0
X Ray Diffraction 3.0733 3.1563 -- 137 7451 0.3014 0.2971 -- 100.0
X Ray Diffraction 3.1563 3.2492 -- 135 7489 0.2934 0.3164 -- 100.0
X Ray Diffraction 3.2492 3.354 -- 140 7471 0.2742 0.3239 -- 100.0
X Ray Diffraction 3.354 3.4738 -- 135 7502 0.2674 0.27 -- 99.0
X Ray Diffraction 3.4738 3.6127 -- 138 7489 0.2575 0.2867 -- 99.0
X Ray Diffraction 3.6127 3.777 -- 133 7440 0.2407 0.2738 -- 99.0
X Ray Diffraction 3.777 3.9759 -- 137 7513 0.2309 0.2458 -- 99.0
X Ray Diffraction 3.9759 4.2247 -- 142 7435 0.21 0.2072 -- 99.0
X Ray Diffraction 4.2247 4.5504 -- 136 7421 0.1946 0.2382 -- 98.0
X Ray Diffraction 4.5504 5.0074 -- 136 7383 0.1906 0.2005 -- 97.0
X Ray Diffraction 5.0074 5.7298 -- 137 7489 0.2032 0.2483 -- 98.0
X Ray Diffraction 5.7298 7.2105 -- 137 7555 0.2103 0.221 -- 97.0
X Ray Diffraction 7.2105 37.5519 -- 134 7358 0.2037 0.2171 -- 92.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 68.5776
Anisotropic B[1][1] 12.2218
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.3698
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -17.5917
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 10.773
f_plane_restr 0.002
f_chiral_restr 0.036
f_angle_d 0.488
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 22127
Nucleic Acid Atoms 0
Heterogen Atoms 84
Solvent Atoms 22

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
RESOLVE version: 2.15 density modification
SOLVE version: 2.13 phasing
SCALEPACK data reduction
DENZO data collection