X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.0
Details potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 104.9 α = 90
b = 109.39 β = 90
c = 181.76 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2010-06-22
Diffraction Radiation
Monochromator Protocol
Double-crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.000 SPring-8 BL38B1

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
3.07 50 99.8 -- 0.079 -- 6.3 40613 40504 0.0 0.0 63.06
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)
3.07 3.18 100.0 -- 0.489 4.5 5.9 4017

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 3.07 38.963 -- 1.34 39714 39710 1994 99.81 0.2707 0.2248 0.2224 0.2707 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 3.07 3.1468 2635 157 2635 0.3006 0.3478 -- 100.0
X Ray Diffraction 3.1468 3.2318 2653 148 2653 0.2731 0.3215 -- 100.0
X Ray Diffraction 3.2318 3.3268 2641 152 2641 0.2542 0.3169 -- 100.0
X Ray Diffraction 3.3268 3.4342 2676 140 2676 0.2445 0.3002 -- 100.0
X Ray Diffraction 3.4342 3.5568 2672 118 2672 0.2309 0.3033 -- 100.0
X Ray Diffraction 3.5568 3.6991 2670 152 2670 0.22 0.2618 -- 100.0
X Ray Diffraction 3.6991 3.8673 2684 135 2684 0.221 0.2825 -- 100.0
X Ray Diffraction 3.8673 4.071 2689 129 2689 0.2173 0.2343 -- 100.0
X Ray Diffraction 4.071 4.3258 2691 152 2691 0.1991 0.2658 -- 100.0
X Ray Diffraction 4.3258 4.6593 2684 145 2684 0.2062 0.2381 -- 100.0
X Ray Diffraction 4.6593 5.1272 2709 136 2709 0.21 0.2932 -- 100.0
X Ray Diffraction 5.1272 5.867 2739 138 2739 0.23 0.2715 -- 100.0
X Ray Diffraction 5.867 7.3835 2752 144 2752 0.2372 0.2998 -- 100.0
X Ray Diffraction 7.3835 38.9656 2821 148 2821 0.1978 0.2191 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 73.5777
Anisotropic B[1][1] 6.4237
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -11.4426
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.0189
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_dihedral_angle_d 27.06
f_chiral_restr 0.065
f_angle_d 1.315
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5945
Nucleic Acid Atoms 5980
Heterogen Atoms 0
Solvent Atoms 0

Software

Software
Software Name Purpose
PHENIX refinement version: 1.7.3_928
PDB_EXTRACT data extraction version: 3.11
BSS data collection
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing