2ZCH | pdb_00002zch

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	1L2E	PDB ENTRY 1L2E, 1RJL
experimental model	PDB	1RJL	PDB ENTRY 1L2E, 1RJL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	293	14% MPEG 550, 100mM HEPES, pH7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.36	α = 90
b = 87.36	β = 90
c = 236.332	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		2006-04-21	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	2.8	78.81	100	0.159	0.168	14.5	9.5		23506

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)
	2.8	2.95	100		0.498	0.525	3.7	9.7	3342

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 1L2E, 1RJL	2.83	78.81	21615	1168	100	0.20652	0.2032	0.21	0.27033	0.27	RANDOM	38.776

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]
0.3			0.3		-0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.157
r_dihedral_angle_3_deg	19.424
r_dihedral_angle_4_deg	17.805
r_dihedral_angle_1_deg	8.083
r_scangle_it	3.072
r_scbond_it	2.043
r_angle_refined_deg	1.874
r_mcangle_it	1.433
r_mcbond_it	1.399
r_angle_other_deg	0.973
r_symmetry_vdw_other	0.256
r_nbd_refined	0.227
r_nbd_other	0.221
r_symmetry_hbond_refined	0.216
r_nbtor_refined	0.191
r_xyhbond_nbd_refined	0.167
r_symmetry_vdw_refined	0.15
r_mcbond_other	0.109
r_chiral_restr	0.103
r_nbtor_other	0.097
r_xyhbond_nbd_other	0.046
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_bond_other_d	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5188
Nucleic Acid Atoms
Solvent Atoms	66
Heterogen Atoms	36

Software

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