4ES6 | pdb_00004es6

Crystal structure of HemD (PA5259) from Pseudomonas aeruginosa (PAO1) at 2.22 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	293	0.1M Na-Cacodylate pH 6.7, 0.87M Na-Citrate , VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.07	α = 90
b = 132.07	β = 90
c = 42.44	γ = 90

Symmetry
Space Group	P 43 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	110	CCD	ADSC QUANTUM 315r	mirrors	2009-10-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.979400	ESRF	ID23-1

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	2.22	66.04	99	0.084	0.084	12	6.3	18993	18993	3.1	3.1	42.1

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)
1	2.22	2.34	95.5		0.539	0.539	3.1	4.3	2611

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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	SAD	THROUGHOUT	2.22	41.76	3.1	3.1	17976	17976	940	98.75	0.21428	0.21234	0.21	0.25183	0.25	RANDOM	39.413

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]
0.37			0.37		-0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.867
r_dihedral_angle_4_deg	16.468
r_dihedral_angle_3_deg	16.398
r_dihedral_angle_1_deg	5.562
r_scangle_it	3.068
r_scbond_it	1.752
r_mcangle_it	1.201
r_angle_refined_deg	1.174
r_mcbond_it	0.625
r_chiral_restr	0.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.867
r_dihedral_angle_4_deg	16.468
r_dihedral_angle_3_deg	16.398
r_dihedral_angle_1_deg	5.562
r_scangle_it	3.068
r_scbond_it	1.752
r_mcangle_it	1.201
r_angle_refined_deg	1.174
r_mcbond_it	0.625
r_chiral_restr	0.071
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1905
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	2

Software

Software
Software Name	Purpose
ADSC	data collection
SHELXS	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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 R01GM157729.