3ROG | pdb_00003rog

Crystal Structure of Mouse Apolipoprotein A-I Binding Protein in Complex with Thymidine 3'-monophosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2O8N	PDB ENTRY 2O8N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	0.1 M SODIUM ACETATE, 1.5 M AMMONIUM SULFATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.094	α = 90
b = 126.094	β = 90
c = 110.962	γ = 120

Symmetry
Space Group	H 3 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	SBC-3	MIRRORS	2008-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	1.04399	APS	19-BM

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	2.05	50	99.8	0.061	0.061	38.741	5.6	119546	119546		-3	35

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	2.05	2.09	99.4		0.361	0.361	3.203	3.6

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 (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 2O8N	2.05	50	21270	1089	99.3	0.18	0.179	0.18	0.201	0.2	RANDOM	55.107

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]
-4.54	-2.27		-4.54		6.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.64
r_dihedral_angle_4_deg	17.589
r_dihedral_angle_3_deg	15.567
r_dihedral_angle_1_deg	6.372
r_scangle_it	4.238
r_angle_other_deg	4.042
r_scbond_it	2.885
r_angle_refined_deg	1.752
r_mcangle_it	1.658
r_mcbond_it	0.971
r_chiral_restr	0.11
r_bond_refined_d	0.021
r_gen_planes_other	0.01
r_gen_planes_refined	0.009
r_bond_other_d
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1808
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing