2ORP

Murine inducible nitric oxide synthase oxygenase domain (delta 114) 2-[4-(2-Imidazol-1-yl-6-methyl-pyrimidin-4-yl)-1-isobutyryl-piperazin-2-yl]-N-[2-(4-methoxy-phenyl)-ethyl]-acetamide complex


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.7
Temperature 308.0
Details CRYSTALS OF MURINE DELTA114 INOS WERE PREPARED IN THE PRESENCE OF IMIDAZOLE FOLLOWING THE PROCEDURES OF CRANE ET AL. (REFERENCE 1) AS FOLLOWS: THE 6 UL CRYSTALLIZATION DROPS CONTAINED 20 MG/ML MURINE DELTA114 INOS, 20 MM HEPES PH 7.6, 5 % GLYCEROL, 0.5 MM DTT, 6.8 % PEG-3350, 60 MM NA2SO3, AND 50 MM IMIDAZOLE/ MALATE BUFFER PH 4.7 WERE PLACED OVER A 1 ML RESERVOIR CONTAINING 13.6 % PEG-3350, 120 MM NA2SO3, AND 100 MM IMIDAZOLE/MALATE BUFFER PH 4.7. THESE CRYSTALS WERE SOAKED FOR 25 HOURS IN 5 UM 2-[4-(2-Imidazol-1-yl-6- methyl-pyrimidin-4-yl)-1-isobutyryl-piperazin-2-yl]-N- [2-(4-methoxy-phenyl)-ethyl]-acetamide, 14 % PEG-3350, 1 MM NAN3, 50 MM MES PH 6.5 AND 50 MM NA2SO3. THE, pH 4.70, VAPOR DIFFUSION, HANGING DROP, temperature 308K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.23 α = 90
b = 73.75 β = 90
c = 93.56 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
IMAGE PLATE MAR scanner 345 mm plate -- 1998-04-09
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 1.08 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
1.97 19.75 95.3 0.09 -- -- 3.6 29604 21034 -- 1.0 20.9
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)
1.97 2.08 95.3 0.289 -- 2.5 3.1 --

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 1.97 19.75 -- 2.0 29604 21034 1179 93.8 0.218 -- 0.217 0.252 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 1.97 2.04 2465 100 2365 0.2715 0.261 0.026 79.0
X Ray Diffraction 2.04 2.12 2916 115 -- 0.2317 0.3272 -- --
X Ray Diffraction 2.12 2.22 2926 130 -- 0.2064 0.2446 -- --
X Ray Diffraction 2.22 2.34 2906 144 -- 0.2145 0.2543 -- --
X Ray Diffraction 2.34 2.48 2918 145 -- 0.2033 0.2068 -- --
X Ray Diffraction 2.48 2.67 2943 121 -- 0.2006 0.2126 -- --
X Ray Diffraction 2.67 2.94 2927 123 -- 0.212 0.2577 -- --
X Ray Diffraction 2.94 3.36 2965 100 -- 0.2207 0.271 -- --
X Ray Diffraction 3.36 4.23 2923 94 -- 0.2016 0.249 -- --
X Ray Diffraction 4.23 19.75 2615 106 2365 0.2361 0.2603 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 36.1
Anisotropic B[1][1] -5.5
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.85
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.34
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.79
c_scbond_it 2.15
c_scangle_it 3.29
c_bond_d 0.007
c_dihedral_angle_d 20.6
c_mcbond_it 1.55
c_mcangle_it 2.54
c_angle_deg 0.9
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Luzzati Sigma A (Observed) 0.15
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.28
Luzzati Sigma A (R-Free Set) 0.14
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2476
Nucleic Acid Atoms 0
Heterogen Atoms 80
Solvent Atoms 201

Software

Software
Software Name Purpose
Blu-Ice data collection
X-PLOR model building
CNS refinement version: 1.1
Blu-Ice data collection
MOSFLM data reduction
CCP4 data scaling version: (SCALA)
X-PLOR phasing