X-RAY DIFFRACTION Experimental Data & Validation


Lost? View more X-Ray Crystallographic info.

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details 20 mg/mL protein, 26% PEG5000 MME, 0.1M MES, 0.1M (NH4)2SO4. Small crystals were used for macroseeding identical conditions, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.22 α = 90
b = 90.43 β = 111.02
c = 70.55 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
AREA DETECTOR ADSC QUANTUM 4 Bent conical Si Mirror (Rh-coated) 2001-09-27
Diffraction Radiation
Monochromator Protocol
Bent Ge (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 1.0 APS 14-BM-C

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
1.73 28.51 94.6 -- 0.069 -- 2.6 69678 65700 0.0 0.0 17.63
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)
1.73 1.77 98.1 -- 0.517 2.11 2.6 --

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 1.727 26.618 -- 0.02 73865 64403 1866 87.19 -- 0.1918 0.1903 0.2423 --
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 1.7274 1.7741 -- 140 4153 0.2566 0.2911 -- 76.0
X Ray Diffraction 1.7741 1.8263 -- 135 4448 0.2493 0.3149 -- 82.0
X Ray Diffraction 1.8263 1.8852 -- 122 4425 0.2432 0.2857 -- 80.0
X Ray Diffraction 1.8852 1.9526 -- 140 4379 0.3172 0.3648 -- 80.0
X Ray Diffraction 1.9526 2.0307 -- 137 4879 0.209 0.257 -- 89.0
X Ray Diffraction 2.0307 2.1231 -- 159 5104 0.1907 0.2376 -- 92.0
X Ray Diffraction 2.1231 2.235 -- 137 5010 0.1866 0.2399 -- 91.0
X Ray Diffraction 2.235 2.3749 -- 135 4775 0.2116 0.3101 -- 87.0
X Ray Diffraction 2.3749 2.5582 -- 151 5171 0.1686 0.1999 -- 93.0
X Ray Diffraction 2.5582 2.8154 -- 155 5172 0.1725 0.2378 -- 94.0
X Ray Diffraction 2.8154 3.2222 -- 150 5175 0.1785 0.2288 -- 93.0
X Ray Diffraction 3.2222 4.0573 -- 154 5013 0.1566 0.2222 -- 91.0
X Ray Diffraction 4.0573 26.6213 -- 151 4833 0.1579 0.1929 -- 86.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.76
Anisotropic B[1][1] -2.4468
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 5.7777
Anisotropic B[2][2] -9.3262
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 11.7729
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.052
f_dihedral_angle_d 15.198
f_angle_d 0.803
f_bond_d 0.004
Coordinate Error
Parameter Value
Luzzati Sigma A (R-Free Set) 0.23
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5486
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 960

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
Deice.py & DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
PHENIX (phenix.refine: 1.6_289) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6_289) refinement
CNS model building
ADSC version: Quantum data collection