2PVS | pdb_00002pvs

Structure of human pancreatic lipase related protein 2 mutant N336Q

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GPL	pdb entry 1GPL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	293	6 microliter of protein (14.5 mg/ml in 0.2 M NaCl, 25 mM Tris-HCl, pH 8.0) and 2 microliter of 2.05 M Ammonium sulphate, 0.1 M Hepes, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.6	65.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 216.181	α = 90
b = 216.181	β = 90
c = 123.672	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 4	mirrors	2007-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3		ESRF	ID14-3

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	3	35	100	0.118	0.118	10.5	6	27791	27791			88

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)
	3	3.16	100		0.48	0.48	1.5	6.1	4339

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 1GPL	3	34.18	27791	27791	1477	99.22	0.1926	0.18966	0.22	0.24948	0.28	RANDOM	51.447

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]
2.43			2.43		-4.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.05
r_dihedral_angle_3_deg	19.065
r_dihedral_angle_4_deg	17.71
r_dihedral_angle_1_deg	7.497
r_scangle_it	1.76
r_angle_refined_deg	1.369
r_scbond_it	1.071
r_angle_other_deg	0.88
r_mcangle_it	0.854
r_mcbond_it	0.496
r_symmetry_hbond_refined	0.33
r_nbd_refined	0.227
r_symmetry_vdw_other	0.208
r_nbd_other	0.198
r_nbtor_refined	0.19
r_symmetry_vdw_refined	0.188
r_xyhbond_nbd_refined	0.174
r_metal_ion_refined	0.156
r_nbtor_other	0.089
r_chiral_restr	0.079
r_mcbond_other	0.078
r_bond_refined_d	0.012
r_bond_other_d	0.004
r_gen_planes_refined	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6868
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing