7BKX | pdb_00007bkx

Diploptera punctata inspired lipocalin-like Milk protein expressed in Saccharomyces cerevisiae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4NYQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	15% of PEG MME 550, 100 mM MES pH 6.5, and 10 mM ZnSO4

Crystal Properties
Matthews coefficient	Solvent content
3.36	63.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.61	α = 90
b = 135.662	β = 90
c = 39.654	γ = 90

Symmetry
Space Group	P 21 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	PIXEL	DECTRIS PILATUS 6M		2019-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.9786	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	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	2.35	20.612	100	0.073	0.998	18.1	12.7		12200

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.39			0.836	0.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4NYQ	2.35	20.6	12161	573	99.77	0.225	0.2222	0.22	0.2782	0.26	58.393

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]
-2.572			1.942		0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.272
r_dihedral_angle_4_deg	25.394
r_dihedral_angle_3_deg	18.236
r_dihedral_angle_1_deg	11.401
r_lrange_it	8.876
r_lrange_other	8.864
r_scangle_it	5.767
r_scangle_other	5.764
r_mcangle_it	4.793
r_mcangle_other	4.79
r_scbond_it	3.519
r_scbond_other	3.517
r_mcbond_it	3.121
r_mcbond_other	3.112
r_angle_refined_deg	2.101
r_angle_other_deg	1.35
r_metal_ion_refined	0.302
r_symmetry_nbd_refined	0.283
r_nbd_refined	0.254
r_xyhbond_nbd_refined	0.211
r_symmetry_nbd_other	0.205
r_nbtor_refined	0.187
r_nbd_other	0.183
r_symmetry_nbtor_other	0.093
r_chiral_restr	0.083
r_symmetry_metal_ion_refined	0.063
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1234
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	97

Software

Software
Software Name	Purpose
xia2	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building