2HB4 | pdb_00002hb4

Structure of HIV Protease NL4-3 in an Unliganded State

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	281.16	100mM Tris HCl, 0.2M MgCl2, 15% PEG 8K, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 281.16K

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.985	α = 90
b = 48.985	β = 90
c = 105.62	γ = 90

Symmetry
Space Group	P 41 21 2

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	RIGAKU SATURN 92	Rigaku VariMax HF Confocal Mirror	2006-05-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU

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	2.15	44.44	99.7	0.095	8.9	7.34	13572	13526	2	3

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	2.15	2.23	99.5		0.601	2.2	7.24	1334

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	THROUGHOUT	2.15	44.46	7074	393	99.57	0.23834	0.23409	0.22	0.32073	0.3	RANDOM	38.072

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]
0.8			0.8		-1.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.988
r_dihedral_angle_4_deg	17.376
r_dihedral_angle_3_deg	17.117
r_dihedral_angle_1_deg	10.26
r_scangle_it	7.613
r_scbond_it	5.677
r_mcangle_it	3.539
r_mcbond_it	2.54
r_angle_refined_deg	2.034
r_symmetry_vdw_refined	0.327
r_nbtor_refined	0.313
r_nbd_refined	0.235
r_xyhbond_nbd_refined	0.211
r_symmetry_hbond_refined	0.191
r_chiral_restr	0.168
r_bond_refined_d	0.023
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	760
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
d*TREK	data scaling