2R9Y | pdb_00002r9y

Structure of antiplasmin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IZ2	PDB entries 1IZ2, 1HP7, 1YXA, 1QMN
experimental model	PDB	1HP7	PDB entries 1IZ2, 1HP7, 1YXA, 1QMN
experimental model	PDB	1YXA	PDB entries 1IZ2, 1HP7, 1YXA, 1QMN
experimental model	PDB	1QMN	PDB entries 1IZ2, 1HP7, 1YXA, 1QMN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.9	296	20% PEG 3350, O.2M MgSO4, 3% sucrose, 1.2% inositol, or 3% trehalose, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
3.99	69.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.679	α = 90
b = 115.679	β = 90
c = 100.533	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV	osmic mirror	2006-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.54

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	2.65	44.95	99.9	0.147	0.059	15.4	7.1		22284

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	2.65		99.9		0.903	0.381	2.1	6.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 entries 1IZ2, 1HP7, 1YXA, 1QMN	2.65	44.95	22284	21122	1139	99.87	0.18605	0.1843	0.1824	0.21798	0.2095	RANDOM	22.436

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]
2.21	1.1		2.21		-3.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.973
r_dihedral_angle_3_deg	16.598
r_dihedral_angle_4_deg	14.955
r_dihedral_angle_1_deg	7.755
r_scangle_it	4.943
r_scbond_it	3.243
r_mcangle_it	2.091
r_angle_refined_deg	1.361
r_mcbond_it	1.119
r_nbtor_refined	0.305
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.199
r_symmetry_hbond_refined	0.151
r_xyhbond_nbd_refined	0.125
r_chiral_restr	0.111
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2834
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASES	phasing