2HBT | pdb_00002hbt

Crystal structure of HIF prolyl hydroxylase EGLN-1 in complex with a biologically active inhibitor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	298	200-300 mM (NH4)2SO4, 100 mM NaOAc pH 4.8-5.4, 22-25% PEG-4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.166	α = 90
b = 111.166	β = 90
c = 40.229	γ = 120

Symmetry
Space Group	P 63

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	MARRESEARCH		2005-08-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

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	1.6	30	96.9	0.019	28.8	4.2	36629	36629			29

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)
	1.6	1.7	98.4		0.261	4.3	2.1	6117

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MIR	THROUGHOUT	1.6	30	36503	36503	1814	96.57	0.214	0.21	0.213	0.2357	0.241	0.2596	RANDOM	27.705

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]
-0.15	-0.07		-0.15		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.553
r_dihedral_angle_3_deg	20.582
r_dihedral_angle_4_deg	17.558
r_dihedral_angle_1_deg	11.27
r_scangle_it	5.77
r_scbond_it	4.638
r_mcangle_it	3.228
r_mcbond_it	2.937
r_angle_refined_deg	1.47
r_mcbond_other	1.079
r_angle_other_deg	0.695
r_symmetry_hbond_refined	0.442
r_symmetry_vdw_other	0.329
r_nbd_refined	0.267
r_nbd_other	0.248
r_xyhbond_nbd_refined	0.213
r_symmetry_vdw_refined	0.212
r_nbtor_refined	0.197
r_chiral_restr	0.118
r_nbtor_other	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1845
Nucleic Acid Atoms
Solvent Atoms	140
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data scaling
SOLVE	phasing