2HKA | pdb_00002hka

Crystal structure of bovine NPC2 and cholesterol sulfate complex

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	5	295	PROTEIN SOLUTION: 10-15 MG/ML CHOLESTEROL SULFATE-BOUND NPC2 IN 0.2 M AMMONIUM ACETATE PH 5.0; WELL SOLUTION: 2.0 M AMMONIUM SULFATE, 0.10 M SODIUM ACETATE PH 5.0, 1.0 MM CETYLTRIMETHYLAMMONIUM BROMIDE, EVAPORATION, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.03	57.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.38	α = 90
b = 62.163	β = 98.62
c = 72.449	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	ENRAF-NONIUS		2005-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A		NSLS	X29A

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	1.81	50	98.2	0.107	17.9	7.5		48283

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	1.81	1.87	93		0.35	4.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (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 1NEP	1.81	20	48241	2431	98.2	0.195	0.19	0.214	0.21	RANDOM

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]
-1.347		-3.644	1.42		-0.073

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	27.1
c_angle_deg	1.38
c_improper_angle_d	1
c_bond_d	0.006
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
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3081
Nucleic Acid Atoms
Solvent Atoms	371
Heterogen Atoms	157

Software

Software
Software Name	Purpose
PHASER	phasing
CNS	refinement