X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 290.0
Details PsaeA.00980.a.B1.PW37585 at 22 mg/ml mixed 1:1 with Morpheus(g9): 10% PEG-20,000, 20% PEG-MME-550, 0.1M bicine/ trizma base, pH=8.5, 0.02M each sodium formate, ammonium acetate, trisodium citrate, sodium potassium L-tartrate, sodium oxamate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.22 α = 90
b = 72.22 β = 90
c = 268.48 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD Beryllium Lenses 2014-12-04
Diffraction Radiation
Monochromator Protocol
Diamond [111] SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

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
2.15 50 99.9 0.044 -- -- 7.3 -- 45360 -- -3.0 42.66
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)
2.15 2.21 100.0 0.543 -- 3.54 7.4 --

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 2.15 40.741 -- 0.0 -- 44182 2199 97.31 -- 0.1813 0.1793 0.2189 --
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 2.1501 2.1968 -- 112 2430 0.2264 0.2805 -- 91.0
X Ray Diffraction 2.1968 2.2479 -- 126 2453 0.2162 0.3098 -- 93.0
X Ray Diffraction 2.2479 2.3041 -- 145 2445 0.2085 0.2484 -- 93.0
X Ray Diffraction 2.3041 2.3664 -- 123 2541 0.2084 0.3158 -- 95.0
X Ray Diffraction 2.3664 2.436 -- 141 2516 0.2036 0.2493 -- 96.0
X Ray Diffraction 2.436 2.5147 -- 146 2574 0.1985 0.2576 -- 97.0
X Ray Diffraction 2.5147 2.6045 -- 126 2621 0.1971 0.2339 -- 98.0
X Ray Diffraction 2.6045 2.7088 -- 185 2561 0.1915 0.2308 -- 99.0
X Ray Diffraction 2.7088 2.832 -- 113 2672 0.2032 0.2776 -- 99.0
X Ray Diffraction 2.832 2.9813 -- 136 2682 0.2125 0.271 -- 99.0
X Ray Diffraction 2.9813 3.168 -- 136 2660 0.2125 0.248 -- 99.0
X Ray Diffraction 3.168 3.4125 -- 149 2692 0.1993 0.2284 -- 100.0
X Ray Diffraction 3.4125 3.7557 -- 138 2722 0.1747 0.236 -- 100.0
X Ray Diffraction 3.7557 4.2987 -- 140 2721 0.1506 0.1752 -- 100.0
X Ray Diffraction 4.2987 5.4138 -- 149 2783 0.143 0.1706 -- 100.0
X Ray Diffraction 5.4138 40.7485 -- 134 2910 0.17 0.1972 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 57.2411
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.111
f_bond_d 0.008
f_plane_restr 0.005
f_dihedral_angle_d 13.168
f_chiral_restr 0.045
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5356
Nucleic Acid Atoms 0
Heterogen Atoms 19
Solvent Atoms 233

Software

Software
Software Name Purpose
XSCALE data scaling
PHENIX refinement
PDB_EXTRACT data extraction version: 3.15
ARP model building