3G9R | pdb_00003g9r

Structure of the HIV-1 gp41 Membrane-Proximal Ectodomain Region in a Putative Prefusion Conformation

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GCM	PDB ENTRY 1GCM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.6	298	0.1M sodium HEPES, 0.1M ammonium dihydrogenphosphate, 50% MPD, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.527	α = 90
b = 48.157	β = 95.38
c = 81.782	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	95	CCD	ADSC QUANTUM 4		2003-03-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.9791	NSLS	X4A

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	19.6	98	0.049	14.1	3.7	22010	22010			39.2

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	2.07	97.5		0.528	2.3	3.6	2171

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 1GCM	2	19.55	22010	22010	1110	98	0.21636	0.21636	0.21347	0.22	0.26908	0.27	RANDOM	57.436

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]
0.93		-0.58	2.96		-4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.858
r_dihedral_angle_3_deg	18.903
r_dihedral_angle_4_deg	18.19
r_dihedral_angle_1_deg	4.795
r_scangle_it	4.446
r_scbond_it	3.441
r_mcangle_it	2.125
r_angle_refined_deg	2.029
r_mcbond_it	1.384
r_nbtor_refined	0.327

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.858
r_dihedral_angle_3_deg	18.903
r_dihedral_angle_4_deg	18.19
r_dihedral_angle_1_deg	4.795
r_scangle_it	4.446
r_scbond_it	3.441
r_mcangle_it	2.125
r_angle_refined_deg	2.029
r_mcbond_it	1.384
r_nbtor_refined	0.327
r_symmetry_hbond_refined	0.289
r_symmetry_vdw_refined	0.287
r_nbd_refined	0.237
r_xyhbond_nbd_refined	0.192
r_chiral_restr	0.139
r_bond_refined_d	0.026
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2241
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms	25

Software

Software
Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

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.