3D4G | pdb_00003d4g

ZP-N domain of mammalian sperm receptor ZP3 (crystal form II)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D4C	PDB ENTRY 3D4C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	Sample: 15mg/ml protein in 0.05M sodium chloride, 0.01M Tris-HCL, PH7.2, 0.001M maltose. Reservoir: 10% PEG6000, 0.2M calcium chloride, 0.1M Tris-HCL, PH7.0. Sample to reservoir ratio in drop: 1:1, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.05	α = 89.99
b = 91.96	β = 90.18
c = 140.48	γ = 89.98

Symmetry
Space Group	P 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		2006-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.95350	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	500	95.4	0.05	11	2	202456	193240		-3	48.357

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.35	95.7		0.529	1.6	2	12935

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3D4C	2.3	50	202438	193225	2139	95.45	0.2017	0.2014	0.2	0.2265	0.23	RANDOM	50.67

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]
-1.23	-0.06	-0.65	0.97	-0.08	0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.357
r_dihedral_angle_4_deg	14.974
r_dihedral_angle_3_deg	12.755
r_dihedral_angle_1_deg	5.525
r_angle_other_deg	4.207
r_scangle_it	1.353
r_angle_refined_deg	0.927
r_scbond_it	0.779
r_mcangle_it	0.778
r_mcbond_it	0.425
r_symmetry_vdw_other	0.264
r_nbd_other	0.217
r_symmetry_vdw_refined	0.209
r_nbd_refined	0.177
r_nbtor_refined	0.169
r_symmetry_hbond_refined	0.156
r_xyhbond_nbd_refined	0.139
r_nbtor_other	0.127
r_metal_ion_refined	0.117
r_chiral_restr	0.051
r_xyhbond_nbd_other	0.042
r_symmetry_metal_ion_refined	0.013
r_bond_refined_d	0.007
r_gen_planes_other	0.003
r_gen_planes_refined	0.002
r_bond_other_d
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	29088
Nucleic Acid Atoms
Solvent Atoms	1934
Heterogen Atoms	208

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
XDS	data scaling