2Z97 | pdb_00002z97

Crystal Structure of Ferric Cytochrome P450cam Reconstituted with 7-Methyl-7-depropionated Hemin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CPP	PDB ENTRY 2CPP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	298	14% PEG 8000, 50mM Tris-HCl, 250mM KCl, 1mM d-camphor, 10mM dithioerythritol(DTE), pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.493	α = 90
b = 66.124	β = 90
c = 104.882	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	100	CCD	Bruker DIP-6040		2007-05-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.7	SPring-8	BL44XU

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	1.8	30.63	100	0.057	5.7	7.5	41567	41567			18.2

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)
	1.8	1.83	100		0.348	4	7.5	2052

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2CPP	1.8	30.63	41567	2085	100	0.15595	0.15347	0.15	0.20277	0.2	RANDOM	20.019

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	34.475
r_dihedral_angle_3_deg	13.898
r_dihedral_angle_4_deg	10.867
r_dihedral_angle_1_deg	5.316
r_scangle_it	2.995
r_scbond_it	1.927
r_angle_refined_deg	1.764
r_mcangle_it	1.238
r_mcbond_it	0.732
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.475
r_dihedral_angle_3_deg	13.898
r_dihedral_angle_4_deg	10.867
r_dihedral_angle_1_deg	5.316
r_scangle_it	2.995
r_scbond_it	1.927
r_angle_refined_deg	1.764
r_mcangle_it	1.238
r_mcbond_it	0.732
r_nbtor_refined	0.311
r_nbd_refined	0.228
r_symmetry_hbond_refined	0.179
r_xyhbond_nbd_refined	0.157
r_metal_ion_refined	0.15
r_symmetry_vdw_refined	0.129
r_chiral_restr	0.126
r_bond_refined_d	0.013
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3208
Nucleic Acid Atoms
Solvent Atoms	713
Heterogen Atoms	51

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.