X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details sodium acetate, CdSO4,CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.57 α = 90
b = 64.59 β = 90
c = 96.01 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 315 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97937 APS 19-ID

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
2.2 30 98.7 -- 0.12 -- 13.9 -- 18873 2.0 2.0 --
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)
2.2 2.5 97.7 -- 0.54 2.4 3.4 1431

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 2.2 28.68 -- -- -- 18872 1017 98.73 -- 0.17941 0.17571 0.2502 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 2.196 2.253 1431 69 1362 0.204 0.272 -- 98.22
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.309
Anisotropic B[1][1] 0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 3.338
r_angle_refined_deg 1.889
r_xyhbond_nbd_refined 0.184
r_nbtor_refined 0.321
r_bond_refined_d 0.022
r_dihedral_angle_4_deg 23.297
r_dihedral_angle_1_deg 6.994
r_dihedral_angle_3_deg 16.181
r_mcangle_it 2.087
r_symmetry_hbond_refined 0.29
r_chiral_restr 0.129
r_nbd_refined 0.219
r_metal_ion_refined 0.115
r_scangle_it 4.903
r_dihedral_angle_2_deg 35.907
r_mcbond_it 1.183
r_gen_planes_refined 0.008
r_symmetry_vdw_refined 0.178
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2801
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 197

Software

Software
Software Name Purpose
HKL-3000 data collection
PHASER phasing
CCP4 model building
REFMAC refinement version: 5.2.0019
HKL-3000 data reduction
HKL-3000 data scaling
CCP4 phasing