3GZE

Algal prolyl 4-hydroxylase complexed with zinc and (Ser-Pro)5 peptide substrate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V4A	PDB ENTRY 2V4A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Microbatch under-oil	5.5	295	5% PEG Smear, 0.1M acetate, 10mM zinc acetate, pH 5.5, Microbatch under-oil, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.62	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 177.25	α = 90
b = 58.75	β = 102.21
c = 105.16	γ = 90

Symmetry
Space Group	C 1 2 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	MARMOSAIC 225 mm CCD		2007-06-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12	0.932	EMBL/DESY, HAMBURG	X12

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	1.98	25	93.4	0.062	12.16	2.9	75581	68688			24.62

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	1.98	2.04	87.1		0.201	4.3	2.5	4412

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 2V4A	1.98	20.6	68677	65243	3434	93.45	0.21888	0.21704	0.25392	RANDOM	11.741

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]
-0.07		1.98	-0.2		1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.487
r_dihedral_angle_4_deg	24.418
r_dihedral_angle_3_deg	16.734
r_dihedral_angle_1_deg	6.514
r_scangle_it	3.327
r_scbond_it	2.289
r_angle_other_deg	2.263
r_angle_refined_deg	1.813
r_mcangle_it	1.393
r_mcbond_it	0.852
r_mcbond_other	0.242
r_chiral_restr	0.101
r_bond_refined_d	0.02
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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	6345
Nucleic Acid Atoms
Solvent Atoms	468
Heterogen Atoms	34

Software

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