2HB6 | pdb_00002hb6

Structure of Caenorhabditis elegans leucine aminopeptidase (LAP1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EWB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	100 MM MES, 2 M AMMONIUM SULFATE, PH 6.00, 5% GLYCEROL, 200 MM SODIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3	58.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.82	α = 90
b = 131.82	β = 90
c = 125.573	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV	MIRRORS	2006-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	50	99.9	0.058	0.093	5.7	12.4	83359	83359

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	99.7		0.423	0.467	1.9	11.7	8253

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	2EWB	2	20	80790	80783	2492	99.93	0.1523	0.14845	0.1474	0.15	0.18279	0.19	RANDOM	26.818

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]
-0.15	-0.07		-0.15		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.13
r_dihedral_angle_4_deg	19.817
r_dihedral_angle_3_deg	14.67
r_scangle_it	7.393
r_dihedral_angle_1_deg	7.314
r_scbond_it	5.476
r_mcangle_it	3.809
r_mcbond_it	2.866
r_angle_refined_deg	1.248
r_nbtor_refined	0.302
r_metal_ion_refined	0.274
r_symmetry_hbond_refined	0.245
r_chiral_restr	0.218
r_xyhbond_nbd_refined	0.185
r_nbd_refined	0.183
r_symmetry_vdw_refined	0.171
r_bond_refined_d	0.011
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_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	7330
Nucleic Acid Atoms
Solvent Atoms	951
Heterogen Atoms	108

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement