X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 290.0
Details 2.9M Sodium Formate, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 181.52 α = 90
b = 184.53 β = 90
c = 186.27 γ = 90
Symmetry
Space Group F 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR MARRESEARCH Mirrors 2001-03-14
Diffraction Radiation
Monochromator Protocol
Yale Mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 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
3 20 -- 0.084 -- -- 2.62 -- 31022 -- -- 70.0
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)
3.0 3.07 -- 0.446 -- 2.25 -- --

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 3.0 20.0 -- 0.0 -- 26609 1425 89.73 0.24557 0.24557 0.24282 0.29506 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 3.0 3.076 -- 98 2019 0.298 0.366 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 62.715
Anisotropic B[1][1] 1.87
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.79
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.07
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.261
r_chiral_restr 0.314
r_dihedral_angle_2_deg 24.784
r_symmetry_vdw_other 0.25
r_gen_planes_other 0.002
r_bond_other_d 0.001
r_xyhbond_nbd_other 0.124
r_xyhbond_nbd_refined 0.219
r_bond_refined_d 0.011
r_symmetry_vdw_refined 0.241
r_symmetry_hbond_refined 0.139
r_angle_refined_deg 1.629
r_dihedral_angle_1_deg 8.342
r_nbd_other 0.239
r_angle_other_deg 1.794
r_gen_planes_refined 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9370
Nucleic Acid Atoms 0
Heterogen Atoms 302
Solvent Atoms 0

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
REFMAC refinement version: 5.0