2Z9A | pdb_00002z9a

Crystal Structure of Human Saposin C Dimer in Open Conformation

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GTG	pdb entry 2gtg

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	291	20 mM NaAcetate, 240 mM magnesium sulfate, 41% (v/v) pentaerythriol ethoxylate 15/4, pH 4.0, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.99	α = 90
b = 48.99	β = 90
c = 155.57	γ = 90

Symmetry
Space Group	P 41 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 4	toroidal mirrors	2004-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.5	25	99.5	0.094	18.83			7088			47.985

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.6	100		0.567	6.3		10030

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		THROUGHOUT	pdb entry 2gtg	2.5	25	10030	7087	335	99.68	0.24	0.239	0.2314	0.271	0.2664	RANDOM	46.373

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]
2.56			2.56		-5.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.389
r_dihedral_angle_3_deg	20.155
r_dihedral_angle_1_deg	4.784
r_scangle_it	2.773
r_scbond_it	1.682
r_angle_refined_deg	1.332
r_mcangle_it	1.154
r_mcbond_it	0.636
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.222
r_nbd_refined	0.211
r_symmetry_hbond_refined	0.202
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.089
r_bond_refined_d	0.011
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1212
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	12

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
MOLREP	phasing