2OXE | pdb_00002oxe

Structure of the Human Pancreatic Lipase-related Protein 2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BU8	PDB ENTRY 1BU8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5	298	1.17M Ammonium sulfate, 0.1M Sodium cacodylate pH 5.5, 0.04M NaCl, cryoprotected with 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 5.50

Crystal Properties
Matthews coefficient	Solvent content
3.5	64.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 216.922	α = 90
b = 216.922	β = 90
c = 123.618	γ = 90

Symmetry
Space Group	I 41 2 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	ADSC QUANTUM 210		2006-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID		APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.8	30	99.3	0.092	12.7	4.1		36137		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	99.1		0.785	2.76	4.1

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 (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 1BU8	2.8	29.88	36116	34305	1811	99.27	0.22432	0.22228	0.22	0.26093	0.25	RANDOM	39.618

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]
4.11			4.11		-8.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.635
r_dihedral_angle_3_deg	17.52
r_dihedral_angle_4_deg	16.8
r_dihedral_angle_1_deg	5.275
r_scangle_it	1.65
r_angle_refined_deg	1.142
r_scbond_it	0.885
r_mcangle_it	0.585
r_mcbond_it	0.322
r_nbtor_refined	0.307
r_nbd_refined	0.201
r_symmetry_vdw_refined	0.169
r_xyhbond_nbd_refined	0.133
r_metal_ion_refined	0.092
r_symmetry_hbond_refined	0.079
r_chiral_restr	0.078
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
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	6642
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	129

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing