X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.8
Temperature 277.0
Details 100mM magnesium acetate, 50mM 2-(N-morpholino)ethanesulfonic acid pH 5.8, 22% 2-methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.92 α = 90
b = 175.8 β = 113.61
c = 93.13 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
CCD RAYONIX MX300HE -- 2011-03-23
Diffraction Radiation
Monochromator Protocol
Horizontally focusing single crystal monochromator (Crystal type Si(1 1 1)) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSRRC BEAMLINE BL13C1 0.97622 NSRRC BL13C1

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 30 97.4 -- 0.08 -- 3.0 65343 63644 1.0 1.0 42.71
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 2.75 98.8 0.467 0.467 2.6 3.1 3232

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 2.7 28.231 -- 1.34 65471 63605 3235 97.15 0.1591 0.1591 0.1562 0.2129 Randomly picked by PHENIX program
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 2.6975 2.7377 -- 118 2561 0.2154 0.2872 -- 93.0
X Ray Diffraction 2.7377 2.7804 -- 152 2627 0.2082 0.2853 -- 99.0
X Ray Diffraction 2.7804 2.826 -- 153 2644 0.1961 0.29 -- 99.0
X Ray Diffraction 2.826 2.8747 -- 141 2632 0.193 0.2323 -- 99.0
X Ray Diffraction 2.8747 2.9269 -- 166 2670 0.1921 0.2767 -- 99.0
X Ray Diffraction 2.9269 2.9831 -- 137 2650 0.1928 0.2727 -- 99.0
X Ray Diffraction 2.9831 3.044 -- 167 2602 0.187 0.2555 -- 98.0
X Ray Diffraction 3.044 3.1101 -- 126 2713 0.1763 0.2678 -- 98.0
X Ray Diffraction 3.1101 3.1823 -- 143 2616 0.1674 0.2308 -- 98.0
X Ray Diffraction 3.1823 3.2618 -- 125 2659 0.165 0.2386 -- 98.0
X Ray Diffraction 3.2618 3.3498 -- 151 2620 0.1558 0.2307 -- 98.0
X Ray Diffraction 3.3498 3.4482 -- 142 2636 0.1572 0.2144 -- 97.0
X Ray Diffraction 3.4482 3.5593 -- 145 2607 0.1443 0.1856 -- 97.0
X Ray Diffraction 3.5593 3.6863 -- 148 2624 0.1477 0.2179 -- 97.0
X Ray Diffraction 3.6863 3.8335 -- 136 2642 0.1459 0.1653 -- 98.0
X Ray Diffraction 3.8335 4.0076 -- 122 2613 0.1458 0.2155 -- 97.0
X Ray Diffraction 4.0076 4.2182 -- 154 2604 0.1321 0.1885 -- 97.0
X Ray Diffraction 4.2182 4.4815 -- 125 2635 0.1246 0.1923 -- 97.0
X Ray Diffraction 4.4815 4.8259 -- 143 2606 0.1288 0.1713 -- 97.0
X Ray Diffraction 4.8259 5.3087 -- 134 2615 0.1454 0.1943 -- 96.0
X Ray Diffraction 5.3087 6.0702 -- 141 2622 0.1671 0.2366 -- 96.0
X Ray Diffraction 6.0702 7.6228 -- 154 2580 0.1674 0.1871 -- 96.0
X Ray Diffraction 7.6228 28.2321 -- 112 2592 0.1498 0.1785 -- 93.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.152
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.074
f_dihedral_angle_d 16.466
f_angle_d 1.192
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10676
Nucleic Acid Atoms 820
Heterogen Atoms 62
Solvent Atoms 426

Software

Computing
Computing Package Purpose
bluice Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX (phenix.automr: 1.6.4_486) Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069) refinement
PHENIX version: (phenix.automr: 1.6.4_486) model building
bluice data collection