X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.4
Details 200 NL OF PROTEIN AT 12 MG/ML IN 1 MM CYCLOSERINE MIXED WITH 200 NL OF RESERVOIR CONSISTING OF 0.1 M HEPES PH 7.5, 150-300 MM NACL AND 22.5-27.5% PEG 4000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.35 α = 105.27
b = 62.12 β = 90.66
c = 119.24 γ = 104.43
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH MULTILAYER MIRROR, VERTICALLY FOCUSING 2011-06-06
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
2.4 30 95.5 0.1 -- -- 2.3 -- 61839 -- 0.0 27.53
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 2.45 82.6 0.5 -- 2.1 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 26.391 -- 1.99 -- 61746 3139 96.39 -- 0.1763 0.1729 0.2394 --
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 2.4 2.4375 -- 147 2541 0.2345 0.3335 -- 92.0
X Ray Diffraction 2.4375 2.4774 -- 117 2688 0.2381 0.3097 -- 96.0
X Ray Diffraction 2.4774 2.5201 -- 132 2624 0.2337 0.3817 -- 96.0
X Ray Diffraction 2.5201 2.5659 -- 127 2674 0.2364 0.3795 -- 96.0
X Ray Diffraction 2.5659 2.6152 -- 140 2651 0.2178 0.346 -- 96.0
X Ray Diffraction 2.6152 2.6685 -- 162 2631 0.2204 0.3231 -- 96.0
X Ray Diffraction 2.6685 2.7265 -- 120 2676 0.2102 0.3048 -- 96.0
X Ray Diffraction 2.7265 2.7898 -- 120 2723 0.2108 0.2876 -- 97.0
X Ray Diffraction 2.7898 2.8595 -- 142 2626 0.1964 0.2859 -- 96.0
X Ray Diffraction 2.8595 2.9368 -- 155 2677 0.1875 0.2769 -- 97.0
X Ray Diffraction 2.9368 3.0231 -- 166 2646 0.1779 0.2538 -- 97.0
X Ray Diffraction 3.0231 3.1205 -- 125 2710 0.1793 0.2591 -- 97.0
X Ray Diffraction 3.1205 3.2318 -- 139 2706 0.1733 0.2265 -- 97.0
X Ray Diffraction 3.2318 3.361 -- 147 2654 0.1733 0.2427 -- 97.0
X Ray Diffraction 3.361 3.5136 -- 156 2684 0.1745 0.2659 -- 97.0
X Ray Diffraction 3.5136 3.6984 -- 164 2658 0.173 0.2339 -- 97.0
X Ray Diffraction 3.6984 3.9294 -- 140 2685 0.1452 0.2016 -- 97.0
X Ray Diffraction 3.9294 4.2317 -- 145 2699 0.1393 0.1955 -- 97.0
X Ray Diffraction 4.2317 4.6554 -- 166 2659 0.1289 0.1772 -- 97.0
X Ray Diffraction 4.6554 5.3242 -- 143 2670 0.1407 0.1989 -- 97.0
X Ray Diffraction 5.3242 6.6899 -- 147 2691 0.1631 0.2056 -- 97.0
X Ray Diffraction 6.6899 26.3927 -- 139 2634 0.1543 0.1687 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 4.487
Anisotropic B[1][2] 4.6434
Anisotropic B[1][3] 2.0306
Anisotropic B[2][2] -1.734
Anisotropic B[2][3] -4.874
Anisotropic B[3][3] -2.753
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.002
f_chiral_restr 0.038
f_dihedral_angle_d 12.732
f_angle_d 0.639
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13841
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 528

Software

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