2QT8 | pdb_00002qt8

Coproporphyrinogen III oxidase from Leishmania major

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VJU	PDB entry 1VJU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	1 ul Protein 11 mg/ml, 1 ul Crystallization buffer: 35% PEG 5000 MME, 200 mM Ammonium sulfate, 100 mM MES pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.083	α = 86.28
b = 53.808	β = 77.28
c = 65.828	γ = 60.99

Symmetry
Space Group	P 1

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	MARMOSAIC 325 mm CCD		2006-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.97930	APS	23-ID-B

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	1.75	46.98	94.6	0.049	15.2	3.3		58682			18.03259

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	1.75	1.81	77		0.229		1.8	4755

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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		THROUGHOUT	PDB entry 1VJU	1.75	20	58641	2958	94.42	0.166	0.165	0.17	0.193	0.2	RANDOM	12.392

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]
-0.21	-0.27	0.52	0.27	0.12	-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.256
r_dihedral_angle_4_deg	12.353
r_dihedral_angle_3_deg	12.045
r_dihedral_angle_1_deg	5.332
r_scangle_it	1.441
r_angle_other_deg	1.194
r_angle_refined_deg	1.027
r_scbond_it	0.96
r_mcangle_it	0.65
r_mcbond_it	0.458
r_symmetry_vdw_other	0.225
r_nbd_refined	0.189
r_nbtor_refined	0.184
r_nbd_other	0.179
r_symmetry_vdw_refined	0.148
r_symmetry_hbond_refined	0.106
r_xyhbond_nbd_refined	0.104
r_nbtor_other	0.084
r_mcbond_other	0.078
r_chiral_restr	0.058
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4875
Nucleic Acid Atoms
Solvent Atoms	532
Heterogen Atoms	12

Software

Software
Software Name	Purpose
TRUNCATE	data reduction
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
REFMAC	refinement