3GKH | pdb_00003gkh

NPC1(NTD)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	294	25% PEG 1500, 100 mM MES Acid, 30 mM Glycine, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.181	α = 90
b = 66.181	β = 90
c = 82.644	γ = 120

Symmetry
Space Group	P 64

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	ADSC QUANTUM 315		2008-08-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID		APS	19-ID

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	1.8	50	98.1	0.08				18538

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.83	98.2

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	SAD	THROUGHOUT	1.81	30.71	17455	956	98.1	0.18189	0.17987	0.18	0.22082	0.23	RANDOM	34.011

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]
0.01			0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.769
r_dihedral_angle_4_deg	16.941
r_dihedral_angle_3_deg	15.583
r_dihedral_angle_1_deg	5.501
r_scangle_it	3.612
r_scbond_it	2.358
r_mcangle_it	1.375
r_angle_refined_deg	1.374
r_mcbond_it	0.821
r_nbtor_refined	0.309
r_nbd_refined	0.206
r_symmetry_vdw_refined	0.15
r_symmetry_hbond_refined	0.146
r_xyhbond_nbd_refined	0.119
r_chiral_restr	0.103
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
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	1749
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement