X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Hanging Drop
pH 10
Temperature 298.0
Details 1% PEG 4000, 5% MPD, 5 mM manganese chloride, 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM glycine, 30 mM sodium acetate with 20% MPD as cryoprotectant, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.19 α = 90
b = 150.77 β = 90
c = 79.4 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS OSMIC BLUE MIRRORS 2012-03-10
Diffraction Radiation
Monochromator Protocol
NI FILTER SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-003 1.54 -- --

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 40 100.0 0.113 -- -- 6.9 -- 17468 -- -- --
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 2.19 100.0 0.483 -- -- 6.9 --

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 20.0 -- -- -- 16566 881 99.82 -- 0.16294 0.15955 0.2253 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 2.15 2.205 -- 55 1089 0.17 0.264 -- 98.28
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.872
Anisotropic B[1][1] -0.04
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.23
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.19
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 19.077
r_dihedral_angle_2_deg 33.084
r_gen_planes_refined 0.009
r_chiral_restr 0.107
r_gen_planes_other 0.001
r_bond_refined_d 0.018
r_dihedral_angle_1_deg 7.456
r_bond_other_d 0.001
r_angle_refined_deg 1.853
r_dihedral_angle_3_deg 15.287
r_angle_other_deg 0.9
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2283
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 156

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.6.0117
PDB_EXTRACT data extraction version: 3.11
CrystalClear data collection
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing