6NF3 | pdb_00006nf3

Structure of the Monoclinic-3 (Monocln-3) Crystal Form of Human Apolipoprotein C1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ROP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	298	The crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs of 16% to 18% 2-methyl-2,4-pentanediol (MPD) containing o.1 M sodium acetate and 0.25% octyl-beta-s-1-thioglucopyanoside. The drops were equal volumes, generally 6 ul each, of the reservoir and an 8 mg/ml solution of protein dissolved in .02 M ammonium bicarbonate.

Crystal Properties
Matthews coefficient	Solvent content
1.74	29.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.169	α = 90
b = 49.965	β = 105.1
c = 35.423	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	AREA DETECTOR	SDMS		1992-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-D	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim 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	2.2	30	70	0.131	0.131	0.15	0.071	0.987	4.6	2.6		5846

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.5	46.2		0.211	0.211	0.295	0.206	0.933	1.7	1.2

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	1ROP	2.33	18.97	4148	226	78.37	0.20485	0.19879	0.21	0.31839	0.32	RANDOM	21.243

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]
7.82		-10.95	9.24		-17.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.207
r_dihedral_angle_4_deg	19.832
r_dihedral_angle_3_deg	17.842
r_long_range_B_refined	5.491
r_long_range_B_other	5.332
r_dihedral_angle_1_deg	4.924
r_mcangle_it	2.246
r_mcangle_other	2.246
r_scangle_other	2.229
r_mcbond_it	1.38
r_mcbond_other	1.375
r_scbond_it	1.33
r_scbond_other	1.329
r_angle_refined_deg	1.093
r_angle_other_deg	0.643
r_chiral_restr	0.053
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	809
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
Aimless	data scaling
PHASER	phasing