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 = 80.55 α = 90
b = 176.61 β = 111.53
c = 93.76 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 -- 2010-12-25
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
2.55 30 99.4 -- 0.07 -- 3.6 79306 78830 1.0 1.0 42.58
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)
2.55 2.59 97.3 0.49 0.49 2.5 3.5 3892

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 2.548 27.941 -- 1.35 79376 78789 3956 99.26 0.1631 0.1631 0.1608 0.206 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 2.5475 2.6384 -- 355 7252 0.2198 0.2855 -- 96.0
X Ray Diffraction 2.6384 2.744 -- 426 7384 0.2062 0.288 -- 98.0
X Ray Diffraction 2.744 2.8687 -- 398 7416 0.1977 0.2627 -- 99.0
X Ray Diffraction 2.8687 3.0198 -- 373 7522 0.1903 0.2566 -- 99.0
X Ray Diffraction 3.0198 3.2088 -- 376 7545 0.1746 0.2344 -- 100.0
X Ray Diffraction 3.2088 3.4561 -- 392 7527 0.1581 0.2091 -- 100.0
X Ray Diffraction 3.4561 3.8031 -- 427 7513 0.1474 0.1927 -- 100.0
X Ray Diffraction 3.8031 4.3517 -- 396 7510 0.1365 0.1712 -- 100.0
X Ray Diffraction 4.3517 5.4759 -- 407 7581 0.141 0.1912 -- 100.0
X Ray Diffraction 5.4759 27.9431 -- 406 7583 0.1605 0.1763 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.3113
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.072
f_dihedral_angle_d 16.507
f_angle_d 1.122
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10722
Nucleic Acid Atoms 820
Heterogen Atoms 70
Solvent Atoms 559

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