2PPL | pdb_00002ppl

Human Pancreatic lipase-related protein 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RP1	PDB ENTRY 1RP1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	291	20% PEG 4000, 0.2M Ca acetate, 0.1 Na cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K, pH 6.50

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.871	α = 90
b = 62.871	β = 90
c = 306.28	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	ADSC QUANTUM 315		2007-03-29	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 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	2.2	40	99.8	0.113	27.6	12.2		32518		-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)
	2.2	2.28	98.9		0.306	4.4	5.7

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-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 1RP1	2.2	35.92	30748	1660	99.75	0.18268	0.18008	0.21	0.23289	0.25	RANDOM	40.03

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]
2.29			2.29		-4.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.496
r_dihedral_angle_4_deg	19.414
r_dihedral_angle_3_deg	15.636
r_scangle_it	6.353
r_dihedral_angle_1_deg	5.936
r_scbond_it	4.561
r_mcangle_it	3.456
r_mcbond_it	2.134
r_angle_refined_deg	1.218
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.212
r_nbd_refined	0.2
r_xyhbond_nbd_refined	0.123
r_metal_ion_refined	0.123
r_symmetry_metal_ion_refined	0.12
r_chiral_restr	0.084
r_symmetry_hbond_refined	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
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_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	3597
Nucleic Acid Atoms
Solvent Atoms	219
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing