4KIA | pdb_00004kia

Crystal structure of LmHde, heme-degrading enzyme, from Listeria monocytogenes

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FEZ	PDB ENTRY 3FEZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5.6	287	25% PEG 3350, 0.1M sodium citrate, 0.2M ammonium sulfate, pH 5.6, MICROBATCH, temperature 287K

Crystal Properties
Matthews coefficient	Solvent content
1.81	32.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 26.61	α = 90
b = 59.474	β = 94.57
c = 45.434	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	ADSC QUANTUM 315r		2009-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0	SPring-8	BL38B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.75	50	99	0.064	30.41	3.6	14344	14209

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	1.75	1.81	94		0.165	0.166	5.78	3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	COOT and PROCHECK	PDB ENTRY 3FEZ	1.75	45.29	14209	13479	713	99.06	0.19101	0.18828	0.1873	0.24432	0.2449	RANDOM	16.237

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]
-0.01			0.04		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.055
r_dihedral_angle_3_deg	12.699
r_dihedral_angle_4_deg	7.734
r_sphericity_free	5.835
r_dihedral_angle_1_deg	5.761
r_scangle_it	4.733
r_scbond_it	3.213
r_sphericity_bonded	3.146
r_mcangle_it	2.023
r_rigid_bond_restr	1.98
r_angle_refined_deg	1.346
r_mcbond_it	1.17
r_chiral_restr	0.091
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1253
Nucleic Acid Atoms
Solvent Atoms	96
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
DM	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
DM	phasing