2ZCL | pdb_00002zcl

Crystal structure of human prostate specific antigen complexed with an activating antibody

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	293	crystals grown in 14% MPEG550, 100mM HEPES (pH7.2), then soaked in 33% PEG400, 100mM MES (pH5.5), 10mM ZnCl2, 0.28mg/ml Mu-KGISSQY-AFC, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.978	α = 90
b = 87.978	β = 90
c = 238.063	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	200	CCD	MARMOSAIC 225 mm CCD		2006-09-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873	ESRF	ID23-2

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	3.25	88.04	99.9	0.144	0.154	14.9	8		15532

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	3.25	3.43	99.4		0.467	0.498	4.9	7.3	2175

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	PDB entry 2ZCH	3.25	82.48	14687	770	99.81	0.20379	0.20139	0.2	0.25098	0.25	RANDOM	65.319

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]
0.36			0.36		-0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.775
r_dihedral_angle_3_deg	22.186
r_dihedral_angle_4_deg	20.201
r_dihedral_angle_1_deg	8.147
r_angle_refined_deg	1.742
r_mcangle_it	1.541
r_mcbond_it	1.197
r_scangle_it	1.11
r_angle_other_deg	0.875
r_scbond_it	0.676
r_nbd_refined	0.221
r_nbd_other	0.213
r_symmetry_vdw_other	0.209
r_symmetry_vdw_refined	0.202
r_nbtor_refined	0.197
r_xyhbond_nbd_refined	0.153
r_mcbond_other	0.135
r_symmetry_hbond_refined	0.119
r_nbtor_other	0.099
r_xyhbond_nbd_other	0.085
r_chiral_restr	0.084
r_bond_refined_d	0.017
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5219
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
MOSFLM	data reduction
PROCESS	data scaling
XFIT	data reduction