6L3A | pdb_00006l3a

Cytochrome P450 107G1 (RapN) with everolimus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4Z5P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		287.15	0.1 M sodium cacodylate, 0.2 M magnesium acetate tetrahydrate, 20% polyethylene glycol 8000

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.028	α = 90
b = 126.142	β = 116.46
c = 70.099	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 315r		2016-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.97940	PAL/PLS	5C (4A)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.5	50	97.3	0.89	18.3	3.2		41761

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.54			0.89	18.3

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	4Z5P	3	44.49	18426	1055	98.88	0.2457	0.2406	0.253	0.3355	0.3395	RANDOM	74.729

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]
-0.19		0.04	-0.03		0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.853
r_dihedral_angle_3_deg	21.654
r_dihedral_angle_4_deg	19.438
r_dihedral_angle_1_deg	8.276
r_angle_refined_deg	1.63
r_angle_other_deg	1.144
r_chiral_restr	0.065
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6082
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	154

Software

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