4JZR

Structure of Prolyl Hydroxylase Domain-containing Protein (PHD) with Inhibitors

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8	293	30% PEG3350, 200mM Ammonium Sulfate, 100mM Sodium Acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.455	α = 90
b = 111.455	β = 90
c = 39.974	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	ADSC QUANTUM 315r		2011-05-29		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.97915	SSRF	BL17U

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	2.1	50	99.8	0.072	14	6.8	16844	16844	2	2

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	2.1	2.14	100		0.558		7.1	822

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.1	50	16805	16805	851	99.6	0.232	0.2306	0.2594	RANDOM	34.541

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]
-0.18	-0.09		-0.18		0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.821
r_dihedral_angle_4_deg	17.489
r_dihedral_angle_3_deg	14.573
r_dihedral_angle_1_deg	6.247
r_scangle_it	2.23
r_angle_refined_deg	1.388
r_scbond_it	1.281
r_mcangle_it	1.276
r_angle_other_deg	0.9
r_mcbond_it	0.665

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.821
r_dihedral_angle_4_deg	17.489
r_dihedral_angle_3_deg	14.573
r_dihedral_angle_1_deg	6.247
r_scangle_it	2.23
r_angle_refined_deg	1.388
r_scbond_it	1.281
r_mcangle_it	1.276
r_angle_other_deg	0.9
r_mcbond_it	0.665
r_chiral_restr	0.079
r_mcbond_other	0.06
r_bond_refined_d	0.008
r_bond_other_d	0.007
r_gen_planes_refined	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1579
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	35

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.