3G4H

Crystal structure of Human Senescence Marker Protein-30 (Zinc Bound)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3G4E	PDB ENTRY 3G4E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.8	298	38% PEG 6000, 0.1M Tris-Hcl, 5mM DTT, 5mM CaCl2, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.365	α = 90
b = 52.019	β = 100.11
c = 85.832	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	100	CCD	MAR CCD 165 mm		2007-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID		APS	31-ID

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	1.92	84.52	99	0.086	0.086	5.251	7		42805

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)
	1.92	2.02	94		0.013	0.01286	0.5	6.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3G4E	1.92	84.52	42738	40630	2108	99.23	0.22519	0.22372	0.25336	RANDOM	43.462

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]
1.9		1.66	1.08		-2.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.287
r_sphericity_free	26.875
r_sphericity_bonded	24.469
r_dihedral_angle_4_deg	21.239
r_dihedral_angle_3_deg	18.166
r_dihedral_angle_1_deg	11.38
r_scangle_it	7.244
r_scbond_it	5.525
r_rigid_bond_restr	4.497
r_mcangle_it	4.362
r_mcbond_it	3.287
r_angle_refined_deg	2.582
r_nbtor_refined	0.314
r_symmetry_vdw_refined	0.291
r_nbd_refined	0.261
r_symmetry_hbond_refined	0.196
r_chiral_restr	0.184
r_xyhbond_nbd_refined	0.176
r_bond_refined_d	0.035
r_gen_planes_refined	0.013
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4606
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	2

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction