4GOH | pdb_00004goh

Structure of the substrate-free HmuO, HO from Corynebacterium diphtheriae

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	PEG8000, Sodium Acetate, Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.489	α = 90
b = 61.916	β = 90
c = 63.086	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 315		2004-10-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	50	98.4			21348	21006

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.86	97.4

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	30	21006	18909	2065	98.26	0.17868	0.17868	0.17471	0.18	0.21615	0.22	RANDOM	20.97

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]
-1.12			-0.3		1.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.499
r_dihedral_angle_3_deg	14.874
r_dihedral_angle_4_deg	13.696
r_dihedral_angle_1_deg	5.544
r_scangle_it	4.426
r_scbond_it	2.796
r_mcangle_it	1.97
r_angle_other_deg	1.838
r_angle_refined_deg	1.729
r_mcbond_it	1.091
r_symmetry_vdw_other	0.356
r_mcbond_other	0.292
r_symmetry_vdw_refined	0.287
r_nbd_refined	0.233
r_nbd_other	0.2
r_metal_ion_refined	0.2
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.123
r_symmetry_hbond_refined	0.123
r_nbtor_other	0.096
r_bond_refined_d	0.019
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
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	1670
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	38

Software

Software
Software Name	Purpose
ADSC	data collection
CNS	refinement
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing