3JX6

Structure of neuronal nitric oxide synthase D597N/M336V/Y706A mutant heme domain complexed with N1-[(3' R,4' R)-4'-((6"-amino-4"-methylpyridin-2"-yl)methyl)pyrrolidin-3'-yl]-N2-(3'-fluorophenethyl)ethane-1,2-diamine tetrahydrochloride


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.8
Temperature 278.0
Details PEG3350, MES, ammonium acetate, SDS, GSH, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 278K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.92 α = 90
b = 111 β = 90
c = 164.18 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 315r mirrors 2009-03-28
Diffraction Radiation
Monochromator Protocol
graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 1.00 SSRL BL7-1

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
2.35 40.81 98.5 0.081 0.081 -- 3.9 -- 39729 -- -3.0 --
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)
2.35 2.39 86.3 0.531 0.531 1.7 3.5 --

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
FOURIER SYNTHESIS 2.35 40.81 -- -- -- 37701 1964 98.39 -- 0.1905 0.18759 0.24535 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 2.35 2.413 -- 126 2374 0.256 0.311 -- 86.18
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 52.128
Anisotropic B[1][1] 0.02
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] -0.03
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 0.598
r_bond_refined_d 0.013
r_chiral_restr 0.097
r_scbond_it 1.916
r_gen_planes_refined 0.006
r_dihedral_angle_3_deg 16.546
r_dihedral_angle_1_deg 5.988
r_angle_refined_deg 1.5
r_dihedral_angle_2_deg 35.158
r_scangle_it 2.999
r_dihedral_angle_4_deg 16.965
r_mcangle_it 1.118
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6642
Nucleic Acid Atoms 0
Heterogen Atoms 183
Solvent Atoms 189

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0089
CNS refinement
ADSC data collection version: Quantum
HKL-2000 data reduction
HKL-2000 data scaling
CNS phasing