2QCI

HIV-1 Protease mutant D30N with potent Antiviral inhibitor GRL-98065


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Z4O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.829825mM sodium acetate, 10% (w/v) sodium chloride, 0.5% dioxane, 1.5% (v/v) dimethylsulfoxide (DMSO), pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.754.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.42α = 90
b = 86.231β = 90
c = 46.008γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2004-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.99997APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.250890.08914.76734116531912.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.21.24510.3682.3423695

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2Z4O1.21065347651213260890.16140.15950.1958RANDOM
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
2716351710.86
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.092
s_similar_adp_cmpnt0.04
s_non_zero_chiral_vol0.036
s_angle_d0.034
s_from_restr_planes0.0304
s_zero_chiral_vol0.028
s_anti_bump_dis_restr0.023
s_bond_d0.013
s_rigid_bond_adp_cmpnt0.004
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1627
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms87

Software

Software
Software NamePurpose
AMoREphasing
SHELXL-97refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling