X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.2
Details PEG3350, HEPES PH7.2, AMMONIUM ACETATE, VAPOR DIFFUSION HANGING DROP, ROOM TEMPERATURE, pH 7.20

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.04 α = 90
b = 71.76 β = 90
c = 71.76 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
IMAGE PLATE RIGAKU IMAGE PLATE MIRRORS 2003-07-31
Diffraction Radiation
Monochromator Protocol
MSC OSMIC BLUE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R -- -- --

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 30 88.6 0.05 -- -- 2.29 -- 18445 -- -- --
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)
2.0 2.07 65.3 0.42 -- 1.6 1.14 --

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 2.1 29.75 -- -- -- 15354 812 100.0 -- 0.235 0.233 0.288 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 2.1 2.15 -- 60 1119 0.282 0.363 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.32
Anisotropic B[1][1] -0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.08
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.1
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.267
r_mcbond_it 1.392
r_symmetry_hbond_refined 0.215
r_gen_planes_refined 0.011
r_scbond_it 3.516
r_symmetry_vdw_refined 0.303
r_dihedral_angle_4_deg 19.864
r_dihedral_angle_3_deg 20.26
r_angle_refined_deg 2.454
r_scangle_it 5.176
r_bond_refined_d 0.028
r_mcangle_it 2.329
r_xyhbond_nbd_refined 0.181
r_dihedral_angle_1_deg 7.831
r_chiral_restr 0.168
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2321
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 60

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.09
CrystalClear data reduction
d*TREK data scaling
MOLREP phasing