3QLH | pdb_00003qlh

HIV-1 Reverse Transcriptase in Complex with Manicol at the RNase H Active Site and TMC278 (Rilpivirine) at the NNRTI Binding Pocket

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZD1	PDB ENTRY 2ZD1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.2	277	Protein solution (20 mg/mL in 9.2 mM Tris pH 8.0, 68.7 mM NaCl, 3.6 mM manganese sulfate, 0.7 mM TCEP, 0.9 mM Manicol, 0.7 mM TMC278, 0.27% BOG, 7% DMSO) Mother Liquor (50 mM HEPES pH 7.5, 100 mM ammonium sulfate, 15 m manganese sulfate, 10 mM spermine, 5 mM TCEP, 11% PEG8000) Cryoprotectant (50 mM HEPES pH 7.5, 50 mM NaCl, 100 mM ammonium sulfate, 15 mM manganese sulfate, 10 mM spermine, 0.69 mM Manicol, 0.34 mM TMC278, 15% PEG8000, 5% PEG400, 10% DMSO, 11% ethylene glycol, 6.5% trimethylamine N-oxide), flash-cooled in LN2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 163.926	α = 90
b = 72.978	β = 101.11
c = 108.377	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315		2009-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25		NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.7	45	99.5	0.063	16.1	6.2	35016	34841	1	1	58.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.75	99		0.707		3.8	1724

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2ZD1	2.7	43.21	34773	33315	995	95.8	0.232	0.232	0.2314	0.22	0.2514	0.24	RANDOM	76.1459

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]
-6.52		-0.64	-0.61		7.13

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25.4
c_scangle_it	8.79
c_mcangle_it	6.97
c_scbond_it	6.61
c_mcbond_it	4.7
c_angle_deg	1.246
c_improper_angle_d	1.15
c_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7885
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	56

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.