3LAM

Crystal structure of HIV-1 reverse transcriptase in complex with N1-propyl pyrimidinedione non-nucleoside inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VRT	pdb entry 1VRT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	1.3M ammonium sulfate, 100mM cacodylate, 5mM sodium malonate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.641	α = 90
b = 154.473	β = 90
c = 153.812	γ = 90

Symmetry
Space Group	C 2 2 21

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		2008-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.0	ALS	5.0.2

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	2.75	50	99.7	0.054	22.8	4.8		36457			57.5

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)
	2.75	2.8	100		0.505	3.1	4.7

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1VRT	2.76	29.91	36403	34539	1716	93.3	0.234	0.231	0.28	RANDOM	70.5

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]
-2.62			-3.66		6.27

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.4
c_scangle_it	3.17
c_mcangle_it	2.83
c_scbond_it	1.96
c_improper_angle_d	1.81
c_angle_deg	1.7
c_mcbond_it	1.61
c_bond_d	0.141
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7842
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	50

Software

Software
Software Name	Purpose
BOS	data collection
EPMR	phasing
CNX	refinement
HKL-2000	data reduction
HKL-2000	data scaling