4NYR | pdb_00004nyr

In-vivo crystallisation (midguts of a viviparous cockroach) and structure at 2.5 A resolution of a glycosylated, lipid-binding, lipocalin-like protein

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	In-vivo crystallization	6	300	Spontaneous crystallization inside the midguts of a living viviparous cockroach, pH 6.0, In-vivo crystallization, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.28	α = 99.5
b = 33.22	β = 100.28
c = 40.18	γ = 104.11

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	70	PIXEL	DECTRIS PILATUS 2M-F		2013-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A	2.7	Photon Factory	BL-1A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.49	50	99.6	38.07	20	5421	5421

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.49	2.56	96.7		22.43		820

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	SAD	THROUGHOUT	2.49	38.58	4876	546	99.83	0.16159	0.16159	0.15368	0.1549	0.23262	0.2322	RANDOM	17.473

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]
-0.25	0.17	-0.05	-0.22	0.38	0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.737
r_dihedral_angle_4_deg	21.681
r_dihedral_angle_3_deg	18.433
r_dihedral_angle_1_deg	7.515
r_long_range_B_refined	5.678
r_mcangle_it	2.031
r_angle_refined_deg	1.906
r_scbond_it	1.836
r_mcbond_it	1.181
r_chiral_restr	0.122

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.737
r_dihedral_angle_4_deg	21.681
r_dihedral_angle_3_deg	18.433
r_dihedral_angle_1_deg	7.515
r_long_range_B_refined	5.678
r_mcangle_it	2.031
r_angle_refined_deg	1.906
r_scbond_it	1.836
r_mcbond_it	1.181
r_chiral_restr	0.122
r_bond_refined_d	0.013
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1248
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms	76

Software

Software
Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.