3V3Y

Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 289.0
Details 3.5% 1,2,3 -heptanetriol, 2% dioxane, 0.1% LDAO, 1M potassium phosphate , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 139.75 α = 90
b = 139.75 β = 90
c = 185.6 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD Bruker Platinum 135 -- 2011-11-11
Diffraction Radiation
Monochromator Protocol
Montel 200 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE BRUKER AXS MICROSTAR 1.54179 -- --

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
2.8 26.6 99.2 0.185 -- -- 3.75 52181 51787 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)
2.8 2.9 99.5 0.626 -- 1.7 3.91 --

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 2.8 19.941 -- 0.0 51787 51655 2640 99.42 0.2465 0.246 0.244 0.284 RANDOM
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 2.8001 2.8508 -- 134 2537 0.3159 0.3716 -- 99.0
X Ray Diffraction 2.8508 2.9055 -- 151 2543 0.2815 0.3315 -- 100.0
X Ray Diffraction 2.9055 2.9646 -- 138 2550 0.2767 0.3245 -- 100.0
X Ray Diffraction 2.9646 3.0289 -- 145 2542 0.2719 0.3205 -- 100.0
X Ray Diffraction 3.0289 3.0991 -- 129 2592 0.2767 0.2992 -- 99.0
X Ray Diffraction 3.0991 3.1763 -- 154 2535 0.2808 0.349 -- 100.0
X Ray Diffraction 3.1763 3.2618 -- 138 2553 0.2771 0.3333 -- 100.0
X Ray Diffraction 3.2618 3.3573 -- 124 2578 0.2878 0.3014 -- 99.0
X Ray Diffraction 3.3573 3.4652 -- 148 2554 0.2786 0.3881 -- 100.0
X Ray Diffraction 3.4652 3.5883 -- 152 2555 0.2789 0.353 -- 100.0
X Ray Diffraction 3.5883 3.7311 -- 132 2555 0.2648 0.2762 -- 99.0
X Ray Diffraction 3.7311 3.8997 -- 153 2543 0.2493 0.271 -- 99.0
X Ray Diffraction 3.8997 4.1036 -- 125 2582 0.2494 0.3036 -- 99.0
X Ray Diffraction 4.1036 4.3582 -- 142 2571 0.2323 0.2934 -- 99.0
X Ray Diffraction 4.3582 4.6907 -- 125 2581 0.2153 0.2241 -- 99.0
X Ray Diffraction 4.6907 5.1553 -- 139 2613 0.2024 0.2303 -- 99.0
X Ray Diffraction 5.1553 5.8845 -- 129 2620 0.2117 0.247 -- 100.0
X Ray Diffraction 5.8845 7.3516 -- 144 2660 0.196 0.2222 -- 100.0
X Ray Diffraction 7.3516 19.9418 -- 138 2751 0.2036 0.2176 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 1.9515
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.9515
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.903
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 20.026
f_chiral_restr 0.09
f_angle_d 1.742
f_plane_restr 0.006
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6482
Nucleic Acid Atoms 0
Heterogen Atoms 696
Solvent Atoms 92

Software

Software
Software Name Purpose
PROTEUM PLUS data collection version: PLUS
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.7.2_869)
PROTEUM PLUS data reduction version: PLUS
PROTEUM PLUS data scaling version: PLUS