X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.1
Temperature 298.0
Details 10% PEG-3350, 100 mM Ca(OAc)2, 100 mM HEPES, 2.5% Glycerol, 250mM sucrose, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.08 α = 90
b = 103.39 β = 101.76
c = 112.99 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 ADSC QUANTUM 315 -- 2011-10-07
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25

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
2.34 30 95.3 0.084 -- -- 2.8 49979 47630 0.0 0.0 --
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)
2.35 2.39 80.7 0.245 -- 3.9 1.7 2002

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 2.338 29.25 -- 1.53 -- 47570 1890 94.1 -- 0.2234 0.2219 0.2586 --
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 2.3382 2.4014 -- 110 2597 0.2998 0.3612 -- 70.0
X Ray Diffraction 2.4014 2.472 -- 140 3299 0.3229 0.3813 -- 89.0
X Ray Diffraction 2.472 2.5517 -- 137 3430 0.2971 0.3752 -- 92.0
X Ray Diffraction 2.5517 2.6429 -- 152 3520 0.3011 0.3234 -- 94.0
X Ray Diffraction 2.6429 2.7486 -- 148 3470 0.29 0.3476 -- 94.0
X Ray Diffraction 2.7486 2.8736 -- 148 3558 0.2878 0.3796 -- 96.0
X Ray Diffraction 2.8736 3.025 -- 148 3609 0.2464 0.3364 -- 97.0
X Ray Diffraction 3.025 3.2143 -- 151 3665 0.2212 0.2535 -- 99.0
X Ray Diffraction 3.2143 3.4621 -- 156 3661 0.2136 0.2561 -- 98.0
X Ray Diffraction 3.4621 3.8098 -- 147 3702 0.2115 0.2503 -- 98.0
X Ray Diffraction 3.8098 4.3596 -- 157 3682 0.1794 0.2095 -- 99.0
X Ray Diffraction 4.3596 5.4867 -- 150 3719 0.1819 0.2156 -- 99.0
X Ray Diffraction 5.4867 29.2519 -- 146 3768 0.2005 0.1829 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -9.1291
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 5.8228
Anisotropic B[2][2] -8.0482
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 17.1773
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.063
f_dihedral_angle_d 19.075
f_angle_d 1.11
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5460
Nucleic Acid Atoms 1378
Heterogen Atoms 52
Solvent Atoms 252

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER in PHENIX Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
PHASER version: in PHENIX model building
CBASS data collection