2Z2T

Crystal structure of the complex between gp41 fragment N36 and fusion inhibitor SC34EK


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4
Temperature 277.0
Details 100mM Sodium Acetate Buffer, pH4.0, 200mM Ammonium Sulphate, 14% PEG2000MME, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 105.01 α = 90
b = 105.01 β = 90
c = 78.31 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU JUPITER 210 -- 2007-04-05
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.000 SPring-8 BL38B1

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
2.1 90 99.7 0.122 -- -- -- -- 29461 -- -- 35.9

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 2.1 19.85 -- -- -- 27843 1494 99.76 -- 0.21464 0.21337 0.23803 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 2.1 2.154 -- 106 2029 0.231 0.255 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.931
Anisotropic B[1][1] 0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.01
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 3.788
r_scbond_it 2.203
r_dihedral_angle_3_deg 15.896
r_mcangle_it 1.228
r_gen_planes_refined 0.003
r_bond_refined_d 0.01
r_chiral_restr 0.075
r_nbtor_refined 0.28
r_dihedral_angle_2_deg 30.11
r_xyhbond_nbd_refined 0.149
r_dihedral_angle_4_deg 18.85
r_scangle_it 3.725
r_nbd_refined 0.183
r_mcbond_it 0.806
r_symmetry_vdw_refined 0.125
r_angle_refined_deg 1.015
r_symmetry_hbond_refined 0.158
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1806
Nucleic Acid Atoms 0
Heterogen Atoms 29
Solvent Atoms 175

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling
AMoRE phasing