5HPG | pdb_00005hpg

STRUCTURE AND LIGAND DETERMINANTS OF THE RECOMBINANT KRINGLE 5 DOMAIN OF HUMAN PLASMINOGEN

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		24% (W/V) PEG 8000, 0.1 M NA-HEPES, PH 7.0, 0.15 M LI2(SO4)

Crystal Properties
Matthews coefficient	Solvent content
2.51	42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.43	α = 90
b = 79.2	β = 90
c = 30.78	γ = 90

Symmetry
Space Group	P 21 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	123	IMAGE PLATE	RIGAKU RAXIS II	MSC-YALE MIRRORS	1997-04-14	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH2R

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	1.66	35.26	72	0.042	0.051	14	2.5		16720		2

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)
	1.6	1.86	37		0.087	0.13	3.6	2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 1PKR	1.66	7	1	16720	15014		84	0.166		15.4

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]

RMS Deviations
Key	Refinement Restraint Deviation
p_transverse_tor	22.4
p_staggered_tor	17.8
p_planar_tor	5.2
p_multtor_nbd	0.24
p_xyhbond_nbd	0.23
p_singtor_nbd	0.18
p_chiral_restr	0.16
p_planar_d	0.05
p_angle_d	0.034
p_bond_d	0.016
p_angle_deg
p_hb_or_metal_coord
p_mcbond_it
p_mcangle_it
p_scbond_it
p_scangle_it
p_plane_restr
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1296
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms

Software

Software
Software Name	Purpose
RIGAKU	data collection
RIGAKU	data reduction
AMoRE	phasing
PROFFT	refinement
R-AXIS	data reduction
R-AXIS	data scaling