1TLB | pdb_00001tlb

Yeast coproporphyrinogen oxidase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	294	2.2 M Ammonium Sulfate, 0.1 M Tris buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.3	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 232.773	α = 90
b = 65.238	β = 107.85
c = 166.071	γ = 90

Symmetry
Space Group	C 1 2 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	IMAGE PLATE	RIGAKU RAXIS IV		1998-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	2.4	30	93.9	0.077	0.077	15	5		83203			38.5

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)
	2.4	2.55	90.7		0.309	0.309	2.5	5	5905

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	Chromium sulfur SAD	THROUGHOUT	2.4	158.11	83203	83203	4402	93.75	0.21189	0.21189	0.20818	0.21	0.28239	0.29	RANDOM	38.507

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]
-1.9		-1.64	3.67		-2.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.308
r_dihedral_angle_4_deg	19.528
r_dihedral_angle_3_deg	18.756
r_dihedral_angle_1_deg	8.407
r_scangle_it	2.928
r_scbond_it	2.057
r_angle_refined_deg	1.832
r_mcangle_it	1.381
r_mcbond_it	1.115
r_angle_other_deg	0.987
r_symmetry_hbond_refined	0.487
r_symmetry_vdw_refined	0.302
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.213
r_symmetry_vdw_other	0.209
r_nbd_other	0.208
r_mcbond_other	0.197
r_nbtor_refined	0.192
r_chiral_restr	0.116
r_nbtor_other	0.096
r_xyhbond_nbd_other	0.08
r_bond_refined_d	0.021
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15886
Nucleic Acid Atoms
Solvent Atoms	640
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing