2HYS | pdb_00002hys

Crystal structure of nitrophorin 2 complexed with cyanide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PEE	pdb entry 1PEE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	89% saturated sodium citrate, 100 mM hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.89	34.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.377	α = 90
b = 34.377	β = 90
c = 257.256	γ = 90

Symmetry
Space Group	P 41 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	MAR CCD 165 mm	bent Si-mirror	2006-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.9795	SSRL	BL9-2

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	1.2	22	84.4	0.05	24	5.4	42640	42640			21.5

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)
	1.2	1.24	85		0.31	3.2	2.6	3225

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	FOURIER SYNTHESIS	THROUGHOUT	pdb entry 1PEE	1.2	22	40513	40513	2127	84.48	0.18715	0.18563	0.18	0.21625	0.21	RANDOM	17.842

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]
-0.36			-0.36		0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.712
r_dihedral_angle_3_deg	13.81
r_dihedral_angle_1_deg	10.883
r_sphericity_free	9.757
r_dihedral_angle_4_deg	8.001
r_sphericity_bonded	6.46
r_scangle_it	5.194
r_scbond_it	3.86
r_mcangle_it	3.123
r_rigid_bond_restr	2.355
r_mcbond_it	2.286
r_angle_refined_deg	2.057
r_nbtor_refined	0.307
r_nbd_refined	0.228
r_symmetry_vdw_refined	0.214
r_symmetry_hbond_refined	0.178
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.143
r_bond_refined_d	0.021
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1453
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
CrystalClear	data reduction
CrystalClear	data scaling