X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 293.0
Details Ammonium Fluoride, PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92 α = 90
b = 67.9 β = 92.97
c = 74.99 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ Osmic Inc. MSC - Blue Confocal Mirrors 2004-10-05
Diffraction Radiation
Monochromator Protocol
Osmic Inc. MSC - Blue Confocal Mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

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
2.5 38 96.2 0.114 -- -- 4.2 16113 15517 0.0 0.0 44.5
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)
2.5 2.56 98.4 0.443 -- 2.9 4.0 1029

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 2.5 37.53 -- 0.0 16113 15517 773 96.31 0.169 0.169 0.164 0.251 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 2.497 2.562 -- 51 973 0.184 0.314 -- 91.02
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 36.501
Anisotropic B[1][1] -0.77
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.44
Anisotropic B[2][2] -0.68
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.3
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 2.412
r_gen_planes_refined 0.007
r_dihedral_angle_3_deg 20.083
r_xyhbond_nbd_refined 0.222
r_nbd_refined 0.237
r_scangle_it 8.094
r_nbtor_refined 0.318
r_symmetry_hbond_refined 0.273
r_bond_refined_d 0.016
r_mcangle_it 3.909
r_scbond_it 5.961
r_dihedral_angle_1_deg 7.137
r_chiral_restr 0.109
r_dihedral_angle_2_deg 35.826
r_dihedral_angle_4_deg 20.202
r_angle_refined_deg 1.999
r_symmetry_vdw_refined 0.265
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3091
Nucleic Acid Atoms 486
Heterogen Atoms 2
Solvent Atoms 213

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
PDB_EXTRACT data extraction version: 1.700
DENZO data reduction
SCALEPACK data scaling
CNS phasing