2RBV | pdb_00002rbv

Cytochrome C Peroxidase in complex with (1-methyl-1h-pyrrol-2-yl)-methylamine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AC4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6	291	MES, MPD, pH 6.0, vapor diffusion, hanging drop, temperature 291K, pH 6.00

Crystal Properties
Matthews coefficient	Solvent content
3.11	60.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.011	α = 90
b = 75.699	β = 90
c = 107.062	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	110	CCD	ADSC QUANTUM 315	KOHZU: DOUBLE CRYSTAL SI(111)	2007-05-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1		ALS	8.3.1

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	1.39	50	99.1	0.045	19.2	3.9		82773

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	1.39	1.44	93.9		0.202		3.4

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		THROUGHOUT	1AC4	1.39	30	82707	82707	4146	99	0.139	0.138	0.14	0.154	0.16	RANDOM	10.85

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]
0.25			0.54		-0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.041
r_dihedral_angle_4_deg	24.407
r_dihedral_angle_3_deg	11.319
r_dihedral_angle_1_deg	5.489
r_sphericity_free	4.327
r_sphericity_bonded	2.44
r_scangle_it	2.206
r_scbond_it	1.7
r_rigid_bond_restr	1.225
r_angle_refined_deg	1.191
r_mcangle_it	1.15
r_mcbond_it	0.958
r_angle_other_deg	0.884
r_mcbond_other	0.386
r_nbd_refined	0.22
r_symmetry_vdw_other	0.22
r_symmetry_hbond_refined	0.216
r_nbd_other	0.187
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.109
r_symmetry_vdw_refined	0.103
r_nbtor_other	0.084
r_chiral_restr	0.078
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2341
Nucleic Acid Atoms
Solvent Atoms	489
Heterogen Atoms	56

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing