X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.5
Details RESERVOIR: 1.5 M NACL, 100 MM NAH2PO4, PH 5.5. SAMPLE: 30 MG/ML PROTEIN IN 50 MM NAH2PO4, PH 6.0.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 71.61 α = 90
b = 79.17 β = 90
c = 113.17 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD (MAR165) MARRESEARCH MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL (R 400 M). 2009-02-19
Diffraction Radiation
Monochromator Protocol
BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING. SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I911-2 -- MAX II I911-2

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
1.8 30 99.7 0.08 -- -- 8.1 -- 30113 -- 4.8 17.86
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)
1.8 1.9 99.0 0.5 -- 4.8 8.0 --

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 1.801 26.554 -- 1.99 -- 30027 1520 99.66 -- 0.1789 0.177 0.2147 --
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 1.8011 1.8592 -- 136 2533 0.2296 0.2694 -- 99.0
X Ray Diffraction 1.8592 1.9257 -- 129 2550 0.2114 0.2491 -- 100.0
X Ray Diffraction 1.9257 2.0027 -- 145 2567 0.1817 0.2449 -- 100.0
X Ray Diffraction 2.0027 2.0938 -- 131 2594 0.1832 0.2128 -- 100.0
X Ray Diffraction 2.0938 2.2042 -- 142 2520 0.1744 0.2349 -- 99.0
X Ray Diffraction 2.2042 2.3422 -- 139 2587 0.1757 0.2287 -- 100.0
X Ray Diffraction 2.3422 2.5229 -- 143 2579 0.1856 0.2328 -- 100.0
X Ray Diffraction 2.5229 2.7766 -- 133 2609 0.191 0.2618 -- 100.0
X Ray Diffraction 2.7766 3.1778 -- 137 2598 0.1821 0.2426 -- 100.0
X Ray Diffraction 3.1778 4.0015 -- 146 2629 0.157 0.1646 -- 100.0
X Ray Diffraction 4.0015 26.5569 -- 139 2741 0.165 0.1819 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 12.5055
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.2078
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -8.2976
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.076
f_dihedral_angle_d 14.043
f_angle_d 1.032
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2511
Nucleic Acid Atoms 0
Heterogen Atoms 8
Solvent Atoms 370

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
PHENIX version: (PHENIX.REFINE) refinement
PHENIX model building