2HZQ | pdb_00002hzq

Crystal structure of human apolipoprotein D (ApoD) in complex with progesterone

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	1.1 M lithium sulfate, 0.1 M ammonium formate, 0.075 M Hepes/NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.206	α = 90
b = 49.206	β = 90
c = 144.126	γ = 90

Symmetry
Space Group	P 43 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	mirrors	2006-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.00890	ESRF	ID23-1

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	1.8	46.575	98.7	0.07	0.07	6.6	11.3	17254	17084		3

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)
	1.8	1.9	95.3		0.308	0.308	2.3	11.2	2350

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	FOURIER SYNTHESIS	THROUGHOUT	1.8	30	17254	17013	860	98.65	0.189	0.189	0.187	0.1863	0.226	0.2216	RANDOM	22.551

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]
0.79			0.79		-1.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.31
r_dihedral_angle_4_deg	22.649
r_dihedral_angle_3_deg	14.28
r_dihedral_angle_1_deg	7.526
r_scangle_it	4.265
r_scbond_it	2.794
r_mcangle_it	1.738
r_angle_refined_deg	1.691
r_mcbond_it	1.107
r_nbtor_refined	0.312
r_symmetry_hbond_refined	0.215
r_nbd_refined	0.21
r_symmetry_vdw_refined	0.193
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.104
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1327
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	23

Software

Software
Software Name	Purpose
SCALA	data scaling
EPMR	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
REFMAC	phasing