5HLF | pdb_00005hlf

STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE In COMPLEX WITH A 38-MER HAIRPIN TEMPLATE-PRIMER DNA APTAMER AND AN ALPHA-CARBOXYPHOSPHONATE INHIBITOR

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5D3G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	7% PEG 8000, 25 MM BISTRIS-PROPANE PH, 6.8, 75 MM BISTRIS-PROPANE PH 7.4, 50 MM AMMONIUM SULFATE, 5% GLYCEROL, 5% SUCROSE

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.06	α = 90
b = 128.56	β = 101.46
c = 132.41	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS3 6M		2015-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.033	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	2.95	43.09	84.8	0.067	0.052	0.989	9.1	2.1		52130			84.87

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.95	3.04	87.5		0.884	0.684	0.471	1.2	2.1	4646

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	FREE R-VALUE	5D3G	2.95	43	1.34	52070	2565	83.57	0.2102	0.2077	0.21	0.2574	0.26	Random selection	103.8995

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.356
f_angle_d	1.434
f_chiral_restr	0.083
f_bond_d	0.011
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15816
Nucleic Acid Atoms	1440
Solvent Atoms	5
Heterogen Atoms	147

Software

Software
Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
Aimless	data scaling
Coot	model building
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHENIX	phasing

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.