2GNI | pdb_00002gni

PKA fivefold mutant model of Rho-kinase with inhibitor Fasudil (HA1077)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		an unpublished structure of the binary complex of PKA C alpha wildtype enzyme with PKI(5-24)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	278	Methanol, LiCl, MesBisTris, EDTA, DTT, Mega8, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
2.56	52.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.227	α = 90
b = 75.959	β = 90
c = 80.396	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	77	CCD	MARRESEARCH		2004-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	1.05	MPG/DESY, HAMBURG	BW6

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.27	30.88	100			21024	21024

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.27	2.39	100

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X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	an unpublished structure of the binary complex of PKA C alpha wildtype enzyme with PKI(5-24)	2.27	30.88	19958	19958	1065	100	0.19222	0.18834	0.1938	0.26817	0.2674	RANDOM	28.473

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]
1.07			0.15		-1.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.241
r_scangle_it	3.567
r_scbond_it	2.204
r_angle_refined_deg	1.596
r_mcangle_it	1.47
r_angle_other_deg	0.88
r_mcbond_it	0.79
r_symmetry_vdw_refined	0.415
r_symmetry_vdw_other	0.301
r_symmetry_hbond_refined	0.283
r_nbd_other	0.24
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.098
r_nbtor_other	0.088
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2978
Nucleic Acid Atoms
Solvent Atoms	217
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing