X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 283.0
Details 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), NBm1 peptide, 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, 1:1 molar ratio with MBM1 peptide, VAPOR DIFFUSION, SITTING DROP, temperature 283K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.6 α = 90
b = 80.06 β = 90
c = 124.55 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D -- APS 21-ID-D

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
1.55 50 98.5 -- 0.076 -- 4.9 -- 70700 -- -- --
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)
1.55 1.58 97.0 -- 0.583 2.1 4.5 --

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 1.55 50.0 -- -- -- 66808 3552 98.56 -- 0.16137 0.15993 0.18855 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 1.55 1.59 -- 259 4565 0.215 0.25 -- 98.05
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.471
Anisotropic B[1][1] 1.51
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.58
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.93
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.02
r_dihedral_angle_3_deg 13.204
r_bond_other_d 0.007
r_dihedral_angle_2_deg 32.444
r_chiral_restr 0.122
r_angle_refined_deg 1.925
r_angle_other_deg 1.081
r_gen_planes_refined 0.011
r_dihedral_angle_1_deg 5.817
r_dihedral_angle_4_deg 16.983
r_gen_planes_other 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3769
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 479

Software

Software
Software Name Purpose
REFMAC refinement version: 5.6.0117