4IMN | pdb_00004imn

Crystal structure of wild type human Lipocalin PGDS bound with PEG MME 2000

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	0.1M potassium thiocyanate, 30% PEG MME 2000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.413	α = 90
b = 56.413	β = 90
c = 72.988	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	199	CCD	ADSC QUANTUM 315		2011-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	0.97622	NSRRC	BL13B1

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	2.09	23.46	94.6	0.073	18.6	4.6	8901	8428		-3	35.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.09	2.16	94.7		0.345	3.23	3.4	824

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	2CZT	2.09	23.46	-3	8427	417	94.65	0.1709	0.16903	0.1779	0.21168	0.2182	RANDOM	35.449

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]
1.99			-1.3		-0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.262
r_dihedral_angle_4_deg	16.666
r_dihedral_angle_3_deg	13.005
r_dihedral_angle_1_deg	6.029
r_angle_refined_deg	1.63
r_angle_other_deg	1.051
r_chiral_restr	0.084
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1208
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms	17

Software

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