X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 290.0
Details 20% PEG2000, 50 mM sodium acetate, 90 mM magnesium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.62 α = 90
b = 62.66 β = 90
c = 65.95 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
CCD ADSC QUANTUM 315 -- 2009-12-11
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 12.3.1 1.1169 ALS 12.3.1

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
1.31 50 98.3 0.049 -- -- 6.7 -- 51271 -- -- --
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)
1.31 1.33 97.8 0.486 -- -- 6.1 2487

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 1.31 39.84 -- 1.35 -- 51213 2612 98.21 -- 0.1356 0.134 0.1643 --
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 1.3097 1.3335 -- 145 2433 0.305 0.3329 -- 96.0
X Ray Diffraction 1.3335 1.3591 -- 120 2555 0.2579 0.3225 -- 98.0
X Ray Diffraction 1.3591 1.3869 -- 147 2485 0.2152 0.2499 -- 99.0
X Ray Diffraction 1.3869 1.417 -- 142 2550 0.177 0.2456 -- 99.0
X Ray Diffraction 1.417 1.45 -- 139 2538 0.1483 0.2185 -- 98.0
X Ray Diffraction 1.45 1.4863 -- 128 2523 0.1207 0.1691 -- 99.0
X Ray Diffraction 1.4863 1.5265 -- 139 2579 0.1097 0.1671 -- 99.0
X Ray Diffraction 1.5265 1.5714 -- 137 2549 0.0973 0.1654 -- 99.0
X Ray Diffraction 1.5714 1.6221 -- 144 2557 0.0953 0.1386 -- 99.0
X Ray Diffraction 1.6221 1.6801 -- 119 2588 0.0966 0.1599 -- 100.0
X Ray Diffraction 1.6801 1.7473 -- 146 2577 0.0973 0.1507 -- 100.0
X Ray Diffraction 1.7473 1.8269 -- 130 2593 0.1067 0.146 -- 100.0
X Ray Diffraction 1.8269 1.9232 -- 130 2581 0.1069 0.1343 -- 100.0
X Ray Diffraction 1.9232 2.0437 -- 134 2604 0.1122 0.1431 -- 100.0
X Ray Diffraction 2.0437 2.2014 -- 148 2600 0.1147 0.1437 -- 100.0
X Ray Diffraction 2.2014 2.423 -- 124 2631 0.1166 0.1322 -- 99.0
X Ray Diffraction 2.423 2.7735 -- 164 2595 0.1305 0.1396 -- 99.0
X Ray Diffraction 2.7735 3.494 -- 145 2656 0.135 0.1646 -- 99.0
X Ray Diffraction 3.494 39.8587 -- 131 2407 0.1776 0.1847 -- 86.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.6598
Anisotropic B[1][1] 1.6479
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.2437
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.8916
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_dihedral_angle_d 14.735
f_bond_d 0.009
f_chiral_restr 0.072
f_angle_d 1.307
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1841
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 303

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.7.1_743
PDB_EXTRACT data extraction version: 3.10
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing