2AEX | pdb_00002aex

The 1.58A Crystal Structure of Human Coproporphyrinogen Oxidase Reveals the Structural Basis of Hereditary Coproporphyria

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	MPD, citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3	60

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.741	α = 90
b = 112.741	β = 90
c = 112.741	γ = 90

Symmetry
Space Group	P 2 3

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 315		2003-12-16	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.9537 0.9795 0.9796	ALS	5.0.2

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	1.5	100				65081	65081		2

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	1.58	1.62	99.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.58	31.31	65081	61787	3294	99.47	0.18709	0.18598	0.2	0.20755	0.2	RANDOM	28.411

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.943
r_dihedral_angle_4_deg	14.636
r_dihedral_angle_3_deg	13.646
r_dihedral_angle_1_deg	5.968
r_scangle_it	2.56
r_mcangle_it	2.268
r_mcbond_it	2.115
r_scbond_it	2.023
r_angle_refined_deg	1.351
r_angle_other_deg	0.768
r_mcbond_other	0.344
r_symmetry_vdw_other	0.246
r_symmetry_vdw_refined	0.228
r_nbd_refined	0.208
r_nbd_other	0.199
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.175
r_symmetry_hbond_refined	0.132
r_nbtor_other	0.086
r_chiral_restr	0.078
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.005
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_refined
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	2702
Nucleic Acid Atoms
Solvent Atoms	363
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHARP	phasing