2ZWU | pdb_00002zwu

Crystal Structure of Camphor Soaked Ferric Cytochrome P450cam

X-RAY DIFFRACTION

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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	11-14% PEG 4000, 50mM Tris-HCl, 250mM KCl, 1mM d-camphor, 10mM dithioerythritol(DTE); After crystallization, soaked camphor saturated buffer for 2 days, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.608	α = 90
b = 63.608	β = 90
c = 250.389	γ = 90

Symmetry
Space Group	P 43 21 2

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	Si	2008-04-22	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	1.3	34.9	98.6	0.075	34.4	4.9		125182			15.597

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)
	1.3	1.35	98.9		0.407	4.9	5	12324

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	1.3	34.9	118839	6277	98.63	0.16644	0.16552	0.17	0.18386	0.18	RANDOM	16.699

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	33.319
r_dihedral_angle_4_deg	14.211
r_dihedral_angle_3_deg	12.511
r_sphericity_bonded	5.878
r_dihedral_angle_1_deg	5.585
r_scangle_it	2.34
r_scbond_it	1.566
r_angle_refined_deg	1.5
r_angle_other_deg	1.354
r_mcangle_it	1.039
r_rigid_bond_restr	0.607
r_mcbond_it	0.575
r_symmetry_vdw_other	0.275
r_nbtor_refined	0.24
r_nbd_other	0.22
r_nbd_refined	0.214
r_symmetry_vdw_refined	0.204
r_nbtor_other	0.175
r_mcbond_other	0.155
r_metal_ion_refined	0.137
r_symmetry_hbond_refined	0.12
r_xyhbond_nbd_refined	0.115
r_chiral_restr	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_free

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4715
Nucleic Acid Atoms
Solvent Atoms	806
Heterogen Atoms	66

Software

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