X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.2
Details 50MM MOPS PH 7.2, 12% MME PEG2K, STREAK-SEEDING

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.02 α = 70.58
b = 64.23 β = 72.81
c = 70.67 γ = 73.84
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU IMAGE PLATE -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

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 20 93.0 0.04 -- -- 2.0 -- 50677 -- -- --
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 2.43 80.0 0.101 -- 7.1 1.8 --

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 2.0 19.8 -- -- -- 48141 2536 100.0 -- -- 0.152 0.194 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 2.0 2.05 -- 128 2635 0.164 0.214 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.47
Anisotropic B[1][1] -0.37
Anisotropic B[1][2] 0.46
Anisotropic B[1][3] 0.09
Anisotropic B[2][2] -0.63
Anisotropic B[2][3] 1.09
Anisotropic B[3][3] -0.03
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.013
r_bond_other_d 0.001
r_dihedral_angle_3_deg 13.99
r_mcbond_it 1.091
r_scbond_it 1.112
r_angle_refined_deg 1.683
r_metal_ion_refined 0.08
r_xyhbond_nbd_refined 0.141
r_mcangle_it 1.8
r_nbtor_other 1.127
r_scangle_it 1.788
r_angle_other_deg 0.854
r_symmetry_hbond_refined 0.149
r_gen_planes_refined 0.006
r_gen_planes_other 0.002
r_symmetry_vdw_other 0.294
r_nbd_refined 0.326
r_symmetry_vdw_refined 0.209
r_chiral_restr 0.108
r_nbd_other 0.238
r_dihedral_angle_1_deg 1.368
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6061
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 596

Software

Software
Software Name Purpose
REFMAC refinement version: 5.0.36
DENZO data reduction
Agrovata data scaling
ROTAVATA data scaling
AMoRE phasing