4CRZ | pdb_00004crz

Direct visualisation of strain-induced protein prost-translational modification

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.4		20% (W/V) POLYETHYLENE GLYCOL (PEG) 3350, 0.1 M BIS-TRIS PROPANE PH 7.4, 0.2 M POTASSIUM THIOCYANATE

Crystal Properties
Matthews coefficient	Solvent content
2.52	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.28	α = 90
b = 86.28	β = 90
c = 80.88	γ = 90

Symmetry
Space Group	I 4

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	IMAGE PLATE	RIGAKU R-AXIS IV	VARIMAX OPTICS	2013-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF

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	1.7	33.7	99.7	0.04	13.3	2.4		32244		2

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	1.7	1.74	99.7		0.4	2.2	2.3

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	PDB ENTRY 4AZD	1.7	29.52	30609	1633	99.59	0.14611	0.14458	0.16	0.17519	0.19	RANDOM	23.383

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]
-0.32			-0.32		0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.68
r_dihedral_angle_4_deg	18.308
r_dihedral_angle_3_deg	16.015
r_dihedral_angle_1_deg	6.591
r_scbond_it	4.172
r_mcangle_it	3.931
r_mcbond_it	2.655
r_mcbond_other	2.652
r_angle_refined_deg	2.333
r_angle_other_deg	0.977
r_chiral_restr	0.144
r_bond_refined_d	0.023
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2002
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms	55

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing