3HNK | pdb_00003hnk

Crystal structure of the dimeric assembly of the cyt cb562 variant RIDC-1

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	26% PEG 2000, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.318	α = 90
b = 55.484	β = 90
c = 72.367	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	APEX II CCD		2008-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	SIEMENS	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.1	36.86	99.5	0.078	0.078	13.4	3.5	12150	12085

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.2	99.5		0.249	0.249	4.1	2.1	1558

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2.1	27.75	12100	12023	830	99.36	0.216	0.205	0.201	0.2063	0.271	0.2705	RANDOM	11.957

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]
					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.034
r_dihedral_angle_3_deg	16.361
r_dihedral_angle_4_deg	15.254
r_dihedral_angle_1_deg	4.225
r_scangle_it	1.908
r_scbond_it	1.217
r_angle_refined_deg	0.994
r_mcangle_it	0.676
r_mcbond_it	0.383
r_nbtor_refined	0.279
r_nbd_refined	0.201
r_symmetry_vdw_refined	0.149
r_xyhbond_nbd_refined	0.145
r_symmetry_hbond_refined	0.145
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_metal_ion_refined	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1638
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
APEX	data collection
SAINT	data reduction
SADABS	data scaling
MOLREP	phasing